diff --git a/weeks/week01/7_tf_binding_promoters.ipynb b/weeks/week01/7_tf_binding_promoters.ipynb index 30395e6..6ffaeff 100644 --- a/weeks/week01/7_tf_binding_promoters.ipynb +++ b/weeks/week01/7_tf_binding_promoters.ipynb @@ -1301,4 +1301,4 @@ }, "nbformat": 4, "nbformat_minor": 0 -} \ No newline at end of file +} diff --git a/weeks/week02/homework2.ipynb b/weeks/week02/homework2.ipynb index 3d439f3..73968e3 100644 --- a/weeks/week02/homework2.ipynb +++ b/weeks/week02/homework2.ipynb @@ -58,7 +58,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 1, "metadata": { "collapsed": false }, @@ -109,7 +109,7 @@ "9 3 8" ] }, - "execution_count": 4, + "execution_count": 1, "metadata": {}, "output_type": "execute_result" } @@ -128,14 +128,29 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 3, "metadata": { "collapsed": false }, "outputs": [ + { + "ename": "ERROR", + "evalue": "Error in file(con, \"rb\"): cannot open the connection\n", + "output_type": "error", + "traceback": [ + "Error in file(con, \"rb\"): cannot open the connection\n" + ] + }, + { + "ename": "ERROR", + "evalue": "Error in file(con, \"rb\"): cannot open the connection\n", + "output_type": "error", + "traceback": [ + "Error in file(con, \"rb\"): cannot open the connection\n" + ] + }, { "data": { - "image/png": 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", "text/plain": [ "plot without title" ] diff --git a/weeks/week03/02_Mann_Whitney.ipynb b/weeks/week03/02_Mann_Whitney.ipynb index 1716c4d..2074769 100644 --- a/weeks/week03/02_Mann_Whitney.ipynb +++ b/weeks/week03/02_Mann_Whitney.ipynb @@ -549,21 +549,11 @@ }, { "cell_type": "code", - "execution_count": 41, + "execution_count": 2, "metadata": { "collapsed": false }, "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "The following objects are masked from ad13b (pos = 5):\n", - "\n", - " cohort.f2, id.f2, normal.f2, nxf1.f2, raw.f2\n", - "\n" - ] - }, { "data": { "text/html": [ @@ -597,7 +587,7 @@ "[1] \"id.f2\" \"nxf1.f2\" \"raw.f2\" \"normal.f2\" \"cohort.f2\"" ] }, - "execution_count": 41, + "execution_count": 2, "metadata": {}, "output_type": "execute_result" } @@ -617,22 +607,28 @@ }, { "cell_type": "code", - "execution_count": 42, + "execution_count": 4, "metadata": { "collapsed": false }, "outputs": [ { - "ename": "ERROR", - "evalue": "Error in stopifnot(is.numeric(x)): object 'normal' not found\n", - "output_type": "error", - "traceback": [ - "Error in stopifnot(is.numeric(x)): object 'normal' not found\n" - ] + "data": { + "text/plain": [ + "\n", + "\tShapiro-Wilk normality test\n", + "\n", + "data: normal.f2[1:6]\n", + "W = 0.63073, p-value = 0.001059\n" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" } ], "source": [ - "shapiro.test(normal[1:6])" + "shapiro.test(normal.f2[1:6])" ] }, { @@ -644,22 +640,28 @@ }, { "cell_type": "code", - "execution_count": 43, + "execution_count": 5, "metadata": { "collapsed": false }, "outputs": [ { - "ename": "ERROR", - "evalue": "Error in stopifnot(is.numeric(x)): object 'normal' not found\n", - "output_type": "error", - "traceback": [ - "Error in stopifnot(is.numeric(x)): object 'normal' not found\n" - ] + "data": { + "text/plain": [ + "\n", + "\tShapiro-Wilk normality test\n", + "\n", + "data: normal.f2[7:12]\n", + "W = 0.92503, p-value = 0.5423\n" + ] + }, + "execution_count": 5, + "metadata": {}, + "output_type": "execute_result" } ], "source": [ - "shapiro.test(normal[7:12])" + "shapiro.test(normal.f2[7:12])" ] }, { @@ -671,22 +673,29 @@ }, { "cell_type": "code", - "execution_count": 44, + "execution_count": 6, "metadata": { "collapsed": false }, "outputs": [ { - "ename": "ERROR", - "evalue": "Error in wilcox.test(normal[1:6], normal[7:12], paired = F, alternative = \"less\"): object 'normal' not found\n", - "output_type": "error", - "traceback": [ - "Error in wilcox.test(normal[1:6], normal[7:12], paired = F, alternative = \"less\"): object 'normal' not found\n" - ] + "data": { + "text/plain": [ + "\n", + "\tWilcoxon rank sum test\n", + "\n", + "data: normal.f2[1:6] and normal.f2[7:12]\n", + "W = 14, p-value = 0.2944\n", + "alternative hypothesis: true location shift is less than 0\n" + ] + }, + "execution_count": 6, + "metadata": {}, + "output_type": "execute_result" } ], "source": [ - "wilcox.test(normal[1:6],normal[7:12],paired=F,alternative=\"less\")" + "wilcox.test(normal.f2[1:6],normal.f2[7:12],paired=F,alternative=\"less\")" ] }, { @@ -698,31 +707,44 @@ }, { "cell_type": "code", - "execution_count": 45, + "execution_count": 7, "metadata": { "collapsed": false }, "outputs": [ { "ename": "ERROR", - "evalue": "Error in eval(expr, envir, enclos): object 'normal' not found\n", + "evalue": "Error in file(con, \"rb\"): cannot open the connection\n", "output_type": "error", "traceback": [ - "Error in eval(expr, envir, enclos): object 'normal' not found\n" + "Error in file(con, \"rb\"): cannot open the connection\n" ] }, { "ename": "ERROR", - "evalue": "Error in eval(expr, envir, enclos): object 'normal' not found\n", + "evalue": "Error in file(con, \"rb\"): cannot open the connection\n", "output_type": "error", "traceback": [ - "Error in eval(expr, envir, enclos): object 'normal' not found\n" + "Error in file(con, \"rb\"): cannot open the connection\n" ] + }, + { + "data": { + "text/plain": [ + "plot without title" + ] + }, + "metadata": { + "image/svg+xml": { + "isolated": true + } + }, + "output_type": "display_data" } ], "source": [ - "plot(normal~nxf1)\n", - "points(normal~nxf1,col=\"darkgreen\")" + "plot(normal.f2~nxf1.f2)\n", + "points(normal.f2~nxf1.f2,col=\"darkgreen\")" ] }, { @@ -734,7 +756,7 @@ }, { "cell_type": "code", - "execution_count": 46, + "execution_count": 8, "metadata": { "collapsed": false }, @@ -743,11 +765,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "The following objects are masked from ad13b (pos = 3):\n", - "\n", - " cohort.f2, id.f2, normal.f2, nxf1.f2, raw.f2\n", - "\n", - "The following objects are masked from ad13b (pos = 6):\n", + "The following objects are masked from ad13b:\n", "\n", " cohort.f2, id.f2, normal.f2, nxf1.f2, raw.f2\n", "\n" @@ -786,7 +804,7 @@ "[1] \"id.f2\" \"nxf1.f2\" \"raw.f2\" \"normal.f2\" \"cohort.f2\"" ] }, - "execution_count": 46, + "execution_count": 8, "metadata": {}, "output_type": "execute_result" } @@ -806,7 +824,7 @@ }, { "cell_type": "code", - "execution_count": 47, + "execution_count": 9, "metadata": { "collapsed": false }, @@ -821,7 +839,7 @@ "W = 0.70643, p-value = 9.494e-05\n" ] }, - "execution_count": 47, + "execution_count": 9, "metadata": {}, "output_type": "execute_result" } @@ -839,7 +857,7 @@ }, { "cell_type": "code", - "execution_count": 48, + "execution_count": 10, "metadata": { "collapsed": false }, @@ -854,7 +872,7 @@ "W = 0.62012, p-value = 0.0001587\n" ] }, - "execution_count": 48, + "execution_count": 10, "metadata": {}, "output_type": "execute_result" } @@ -940,39 +958,38 @@ }, { "cell_type": "code", - "execution_count": 51, + "execution_count": 12, "metadata": { "collapsed": false }, "outputs": [ { - "ename": "ERROR", - "evalue": "Error in eval(expr, envir, enclos): object 'normal' not found\n", - "output_type": "error", - "traceback": [ - "Error in eval(expr, envir, enclos): object 'normal' not found\n" - ] - }, - { - "ename": "ERROR", - "evalue": "Error in eval(expr, envir, enclos): object 'normal' not found\n", - "output_type": "error", - "traceback": [ - "Error in eval(expr, envir, enclos): object 'normal' not found\n" + "name": "stderr", + "output_type": "stream", + "text": [ + "Warning message:\n", + "In wilcox.test.default(grpB, grpC, paired = F, alternative = \"less\"): cannot compute exact p-value with ties" ] }, { - "ename": "ERROR", - "evalue": "Error in wilcox.test(grpB, grpC, paired = F, alternative = \"less\"): object 'grpB' not found\n", - "output_type": "error", - "traceback": [ - "Error in wilcox.test(grpB, grpC, paired = F, alternative = \"less\"): object 'grpB' not found\n" - ] + "data": { + "text/plain": [ + "\n", + "\tWilcoxon rank sum test with continuity correction\n", + "\n", + "data: grpB and grpC\n", + "W = 124, p-value = 0.00999\n", + "alternative hypothesis: true location shift is less than 0\n" + ] + }, + "execution_count": 12, + "metadata": {}, + "output_type": "execute_result" } ], "source": [ - "grpB<-c(normal.f2[1:18],normal[1:6])\n", - "grpC<-c(normal.f2[19:30],normal[7:12])\n", + "grpB<-c(normal.f2[1:18],normal.f2[1:6])\n", + "grpC<-c(normal.f2[19:30],normal.f2[7:12])\n", "wilcox.test(grpB,grpC,paired=F,alternative=\"less\")" ] }, @@ -985,18 +1002,39 @@ }, { "cell_type": "code", - "execution_count": 52, + "execution_count": 13, "metadata": { "collapsed": false }, "outputs": [ { "ename": "ERROR", - "evalue": "Error in boxplot(grpB, grpC): object 'grpB' not found\n", + "evalue": "Error in file(con, \"rb\"): cannot open the connection\n", + "output_type": "error", + "traceback": [ + "Error in file(con, \"rb\"): cannot open the connection\n" + ] + }, + { + "ename": "ERROR", + "evalue": "Error in file(con, \"rb\"): cannot open the connection\n", "output_type": "error", "traceback": [ - "Error in boxplot(grpB, grpC): object 'grpB' not found\n" + "Error in file(con, \"rb\"): cannot open the connection\n" ] + }, + { + "data": { + "text/plain": [ + "plot without title" + ] + }, + "metadata": { + "image/svg+xml": { + "isolated": true + } + }, + "output_type": "display_data" } ], "source": [ diff --git a/weeks/week03/homework.ipynb b/weeks/week03/homework.ipynb index 9a17a19..607dc81 100644 --- a/weeks/week03/homework.ipynb +++ b/weeks/week03/homework.ipynb @@ -23,7 +23,7 @@ "cell_type": "raw", "metadata": {}, "source": [ - " " + "Two-tailed, becuase relative gene expression could go in either direction (up or down)" ] }, { @@ -36,7 +36,9 @@ { "cell_type": "raw", "metadata": {}, - "source": [] + "source": [ + "Mann-Whitney U Test/Wilcoxon rank sum test The data are not explicitly paired, thus the Wilcoxon signed rank test cannot be used. Tha data do fit the assumptions of the Mann-Whitney U Test/Wilcoxon rank sum test however." + ] }, { "cell_type": "markdown", @@ -46,9 +48,285 @@ ] }, { - "cell_type": "raw", - "metadata": {}, - "source": [] + "cell_type": "code", + "execution_count": 3, + "metadata": { + "collapsed": false + }, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "The following objects are masked from b6 (pos = 3):\n", + "\n", + " cohort, id, normal, nxf1, raw\n", + "\n" + ] + }, + { + "data": { + "text/html": [ + "
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\n" + ], + "text/latex": [ + "\\begin{tabular}{r|lllll}\n", + " & id.f2 & nxf1.f2 & raw.f2 & normal.f2 & cohort.f2\\\\\n", + "\\hline\n", + "\t1 & EB026 & B & 7e-05 & 0.000740424 & 4/3/09\\\\\n", + "\t2 & EB211 & B & 0.00012 & 0.001157392 & 4/3/09\\\\\n", + "\t3 & EB030 & B & 0.00014 & 0.001380945 & 4/3/09\\\\\n", + "\t4 & EB034 & B & 0.00022 & 0.002208735 & 4/3/09\\\\\n", + "\t5 & EB319 & B & 0.00091 & 0.009084916 & 4/3/09\\\\\n", + "\t6 & EB189 & B & 0.00213 & 0.001081516 & 4/15/09\\\\\n", + "\t7 & EB237 & B & 0.0031 & 0.001573233 & 4/15/09\\\\\n", + "\t8 & EB279 & B & 0.00349 & 0.001772814 & 4/15/09\\\\\n", + "\t9 & EB222 & B & 0.00372 & 0.001890922 & 4/15/09\\\\\n", + "\t10 & EB342 & B & 0.00214 & 0.001334754 & 4/16/09\\\\\n", + "\t11 & EB299 & B & 0.00217 & 0.001349456 & 4/16/09\\\\\n", + "\t12 & EB336 & B & 0.00271 & 0.001686254 & 4/16/09\\\\\n", + "\t13 & EB326 & B & 0.00289 & 0.001800217 & 4/16/09\\\\\n", + "\t14 & EB319 & B & 0.00327 & 0.002037232 & 4/16/09\\\\\n", + "\t15 & EB338 & B & 0.00335 & 0.002086975 & 4/16/09\\\\\n", + "\t16 & EB362 & B & 0.00657 & 0.004091404 & 4/16/09\\\\\n", + "\t17 & EB321 & B & 0.00776 & 0.004834029 & 4/16/09\\\\\n", + "\t18 & EB323 & B & 0.01112 & 0.006926883 & 4/16/09\\\\\n", + "\t19 & EB032 & C & 0.00037 & 0.00369398 & 4/3/09\\\\\n", + "\t20 & EB346 & C & 0.00055 & 0.00547956 & 4/3/09\\\\\n", + "\t21 & EB217 & C & 0.00063 & 0.006311733 & 4/3/09\\\\\n", + "\t22 & EB297 & C & 0.00445 & 0.002261018 & 4/15/09\\\\\n", + "\t23 & EB266 & C & 0.00558 & 0.00283316 & 4/15/09\\\\\n", + "\t24 & EB265 & C & 0.00596 & 0.003029921 & 4/15/09\\\\\n", + "\t25 & EB241 & C & 0.00627 & 0.003188702 & 4/15/09\\\\\n", + "\t26 & EB278 & C & 0.00891 & 0.00453021 & 4/15/09\\\\\n", + "\t27 & EB225 & C & 0.01061 & 0.005392136 & 4/15/09\\\\\n", + "\t28 & EB294 & C & 0.01089 & 0.005533425 & 4/15/09\\\\\n", + "\t29 & EB305 & C & 0.01459 & 0.009084457 & 4/16/09\\\\\n", + "\t30 & EB340 & C & 0.03784 & 0.02356012 & 4/16/09\\\\\n", + "\t31 & EB216 & H & 0.00022 & 0.002160174 & 4/3/09\\\\\n", + "\\end{tabular}\n" + ], + "text/plain": [ + " id.f2 nxf1.f2 raw.f2 normal.f2 cohort.f2\n", + "1 EB026 B 0.00007 0.000740424 4/3/09\n", + "2 EB211 B 0.00012 0.001157392 4/3/09\n", + "3 EB030 B 0.00014 0.001380945 4/3/09\n", + "4 EB034 B 0.00022 0.002208735 4/3/09\n", + "5 EB319 B 0.00091 0.009084916 4/3/09\n", + "6 EB189 B 0.00213 0.001081516 4/15/09\n", + "7 EB237 B 0.00310 0.001573233 4/15/09\n", + "8 EB279 B 0.00349 0.001772814 4/15/09\n", + "9 EB222 B 0.00372 0.001890922 4/15/09\n", + "10 EB342 B 0.00214 0.001334754 4/16/09\n", + "11 EB299 B 0.00217 0.001349456 4/16/09\n", + "12 EB336 B 0.00271 0.001686254 4/16/09\n", + "13 EB326 B 0.00289 0.001800217 4/16/09\n", + "14 EB319 B 0.00327 0.002037232 4/16/09\n", + "15 EB338 B 0.00335 0.002086975 4/16/09\n", + "16 EB362 B 0.00657 0.004091404 4/16/09\n", + "17 EB321 B 0.00776 0.004834029 4/16/09\n", + "18 EB323 B 0.01112 0.006926883 4/16/09\n", + "19 EB032 C 0.00037 0.003693980 4/3/09\n", + "20 EB346 C 0.00055 0.005479560 4/3/09\n", + "21 EB217 C 0.00063 0.006311733 4/3/09\n", + "22 EB297 C 0.00445 0.002261018 4/15/09\n", + "23 EB266 C 0.00558 0.002833160 4/15/09\n", + "24 EB265 C 0.00596 0.003029921 4/15/09\n", + "25 EB241 C 0.00627 0.003188702 4/15/09\n", + "26 EB278 C 0.00891 0.004530210 4/15/09\n", + "27 EB225 C 0.01061 0.005392136 4/15/09\n", + "28 EB294 C 0.01089 0.005533425 4/15/09\n", + "29 EB305 C 0.01459 0.009084457 4/16/09\n", + "30 EB340 C 0.03784 0.023560116 4/16/09\n", + "31 EB216 H 0.00022 0.002160174 4/3/09" + ] + }, + "execution_count": 17, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "f2<-read.table (\"adamts_balbF2.txt\", head=T)\n", + "attach (f2)\n", + "names (f2)\n", + "f2" + ] + }, + { + "cell_type": "code", + "execution_count": 19, + "metadata": { + "collapsed": false + }, + "outputs": [ + { + "data": { + "text/plain": [ + "\n", + "\tWilcoxon rank sum test\n", + "\n", + "data: normal.f2[1:18] and normal.f2[19:30]\n", + "W = 32, p-value = 0.0003972\n", + "alternative hypothesis: true location shift is less than 0\n" + ] + }, + "execution_count": 19, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "wilcox.test(normal.f2[1:18],normal.f2[19:30],paired=F,alternative=\"less\")" + ] }, { "cell_type": "markdown", @@ -74,7 +549,9 @@ { "cell_type": "raw", "metadata": {}, - "source": [] + "source": [ + "The C allele of Nfx1 causes an increase in expression of gene 8. The evidence is fairly strong since both independent sets of experiments found this same conclusion at a p-value of less than 0.05. THe evidence would have been much weaker if only one such set of experiments existed." + ] }, { "cell_type": "markdown", @@ -86,7 +563,9 @@ { "cell_type": "raw", "metadata": {}, - "source": [] + "source": [ + "parametric tests are in general more sensitive to outliers because they assume a specific distribution of data" + ] }, { "cell_type": "markdown", diff --git a/weeks/week04/0_alignment_expression_quantification.ipynb b/weeks/week04/0_alignment_expression_quantification.ipynb index 4e241be..21d2111 100644 --- a/weeks/week04/0_alignment_expression_quantification.ipynb +++ b/weeks/week04/0_alignment_expression_quantification.ipynb @@ -270,7 +270,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 1, "metadata": { "collapsed": false, "deletable": false, @@ -282,7 +282,18 @@ "solution": false } }, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "25" + ] + }, + "execution_count": 1, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "5**2" ] @@ -305,7 +316,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 5, "metadata": { "collapsed": false, "deletable": false, @@ -317,14 +328,25 @@ "solution": false } }, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "73" + ] + }, + "execution_count": 5, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "ord('I')" ] }, { "cell_type": "code", - "execution_count": null, + "execution_count": 3, "metadata": { "collapsed": false, "deletable": false, @@ -336,7 +358,18 @@ "solution": false } }, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "33" + ] + }, + "execution_count": 3, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "ord('!')" ] @@ -359,7 +392,11 @@ }, { "cell_type": "code", +<<<<<<< HEAD + "execution_count": 8, +======= "execution_count": 3, +>>>>>>> 3763db8983f51be4f5e2a40d9b92af6d0e25f41f "metadata": { "collapsed": false, "deletable": false, @@ -384,7 +421,13 @@ } ], "source": [ +<<<<<<< HEAD + "q = ord('A') -33\n", + "\n", + "p = 10**(-q/10)" +======= "10**(-(ord(\"A\") - ord(\"!\"))/10)" +>>>>>>> 3763db8983f51be4f5e2a40d9b92af6d0e25f41f ] }, { @@ -534,8 +577,16 @@ "Make directories in scratch:\n", "\n", "```\n", +<<<<<<< HEAD + "/home/ucsd-train##/projects\n", + "/home/ucsd-train##/projects/shalek2013\n", + "/home/ucsd-train##/projects/shalek2013/processing_scripts\n", + "/home/ucsd-train##/projects/shalek2013/raw_data\n", + "/home/ucsd-train##/scratch/shalek2013/processed_data\n", +======= "mkdir $HOME/scratch/shalek2013\n", "mkdir $HOME/scratch/shalek2013/processed_data\n", +>>>>>>> 3763db8983f51be4f5e2a40d9b92af6d0e25f41f "```\n", "\n", "### Exercise 4: Create soft links\n", @@ -697,7 +748,11 @@ } }, "source": [ +<<<<<<< HEAD + "kallisto quant --single -l (average fragment length)" +======= "--single --fragment-length=200.1" +>>>>>>> 3763db8983f51be4f5e2a40d9b92af6d0e25f41f ] }, { @@ -762,7 +817,7 @@ "Read about the [SAM](https://samtools.github.io/hts-specs/SAMv1.pdf) format and check out [this](https://broadinstitute.github.io/picard/explain-flags.html) helpful website for explaining SAM flags.\n", "\n", "1. Which file would you use to get the percentage of mapped reads from your data?\n", - "2. Which file would you send to someone when the alignment didn't go as expected and thye asked for the parameters you used?\n", + "2. Which file would you send to someone when the alignment didn't go as expected and they asked for the parameters you used?\n", "\n", "To view the SAM file, you'll want to use `samtools`. Viewing directly with `head` gives you the \"header\" of the SAM file which has a bunch of parameters about the genome and the program that was used to align:\n", "\n", @@ -812,7 +867,11 @@ }, "source": [ "1. S10.Log.final.out\n", +<<<<<<< HEAD + "2. your original .sh script\n" +======= "2. S10.Log.out" +>>>>>>> 3763db8983f51be4f5e2a40d9b92af6d0e25f41f ] }, { @@ -857,9 +916,15 @@ } }, "source": [ +<<<<<<< HEAD + "1. --input-fmt-sam\n", + "2. -b\n", + "3. --threads" +======= "1. -S\n", "2. -b\n", "3. -@ 4" +>>>>>>> 3763db8983f51be4f5e2a40d9b92af6d0e25f41f ] }, { diff --git a/weeks/week04/2_compare_alignment_vs_quasialignment.ipynb b/weeks/week04/2_compare_alignment_vs_quasialignment.ipynb index 6c9fe1a..cc3c996 100644 --- a/weeks/week04/2_compare_alignment_vs_quasialignment.ipynb +++ b/weeks/week04/2_compare_alignment_vs_quasialignment.ipynb @@ -41,7 +41,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 23, "metadata": { "collapsed": false, "deletable": false, @@ -53,7 +53,16 @@ "solution": false } }, - "outputs": [], + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/home/ucsd-train12/anaconda3/lib/python3.5/site-packages/matplotlib/__init__.py:872: UserWarning: axes.color_cycle is deprecated and replaced with axes.prop_cycle; please use the latter.\n", + " warnings.warn(self.msg_depr % (key, alt_key))\n" + ] + } + ], "source": [ "# We're doing \"import superlongname as abbrev\" for our laziness - this way we don't have to type out the whole thing each time.\n", "\n", @@ -71,6 +80,7 @@ "\n", "sns.set(style='ticks', context='notebook')\n", "\n", + "\n", "# This is necessary to show the plotted figures inside the notebook -- \"inline\" with the notebook cells\n", "%matplotlib inline" ] @@ -93,7 +103,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 2, "metadata": { "collapsed": false, "deletable": false, @@ -105,7 +115,15 @@ "solution": false } }, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "/oasis/tscc/scratch/ucsd-train12/shalek2013/processed_data\n" + ] + } + ], "source": [ "cd ~/projects/shalek2013/processed_data" ] @@ -128,7 +146,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 35, "metadata": { "collapsed": false, "deletable": false, @@ -140,7 +158,91 @@ "solution": false } }, - "outputs": [], + "outputs": [ + { + "data": { + "text/html": [ + "
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lengtheff_lengthest_countstpm
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lengtheff_lengthest_countstpm
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lengtheff_lengthest_countstpm
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ENSMUST00000192650.5|ENSMUSG00000025902.13|OTTMUSG00000050014.7|OTTMUST00000127247.2|Sox17-004|Sox17|3242|UTR5:1-1851|CDS:1852-2916|UTR3:2917-3242|32422997.5800.000000.000000
ENSMUST00000116652.7|ENSMUSG00000025902.13|OTTMUSG00000050014.7|OTTMUST00000127246.1|Sox17-002|Sox17|1512|UTR5:1-249|CDS:250-1509|UTR3:1510-1512|15121267.5800.000000.000000
ENSMUST00000191647.1|ENSMUSG00000025902.13|OTTMUSG00000050014.7|OTTMUST00000127267.2|Sox17-007|Sox17|406|UTR5:1-83|CDS:84-406|406163.2700.000000.000000
ENSMUST00000191939.1|ENSMUSG00000025902.13|OTTMUSG00000050014.7|OTTMUST00000127266.2|Sox17-006|Sox17|840|UTR5:1-329|CDS:330-840|840595.5790.000000.000000
ENSMUST00000192913.1|ENSMUSG00000025902.13|OTTMUSG00000050014.7|OTTMUST00000127248.2|Sox17-003|Sox17|1506|UTR5:1-997|CDS:998-1506|15061261.5800.000000.000000
ENSMUST00000130201.7|ENSMUSG00000033845.13|OTTMUSG00000029329.3|OTTMUST00000072660.1|Mrpl15-002|Mrpl15|1894|UTR5:1-33|CDS:34-648|UTR3:649-1894|18941649.58010.000000.212263
ENSMUST00000156816.6|ENSMUSG00000033845.13|OTTMUSG00000029329.3|OTTMUST00000072659.1|Mrpl15-001|Mrpl15|4203|UTR5:1-62|CDS:63-950|UTR3:951-4203|42033958.5800.000000.000000
ENSMUST00000045689.13|ENSMUSG00000033845.13|OTTMUSG00000029329.3|OTTMUST00000072661.1|Mrpl15-003|Mrpl15|497|UTR5:1-21|CDS:22-180|UTR3:181-497|497252.8040.000000.000000
ENSMUST00000146665.2|ENSMUSG00000033845.13|OTTMUSG00000029329.3|OTTMUST00000072662.2|Mrpl15-004|Mrpl15|1569|UTR5:1-62|CDS:63-569|UTR3:570-1569|15691324.5800.000000.000000
ENSMUST00000134384.7|ENSMUSG00000025903.14|OTTMUSG00000021562.4|OTTMUST00000051163.2|Lypla1-002|Lypla1|1136|UTR5:1-126|CDS:127-801|UTR3:802-1136|1136891.5795.425560.213075
ENSMUST00000027036.10|ENSMUSG00000025903.14|OTTMUSG00000021562.4|OTTMUST00000051162.1|Lypla1-001|Lypla1|2507|UTR5:1-91|CDS:92-784|UTR3:785-2507|25072262.580518.909008.030360
ENSMUST00000150971.7|ENSMUSG00000025903.14|OTTMUSG00000021562.4|OTTMUST00000051164.3|Lypla1-003|Lypla1|877|UTR5:1-84|CDS:85-750|UTR3:751-877|877632.5790.000000.000000
\n", + "
" + ], + "text/plain": [ + " length eff_length \\\n", + "target_id \n", + "ENSMUST00000070533.4|ENSMUSG00000051951.5|OTTMU... 3634 3389.580 \n", + "ENSMUST00000194992.5|ENSMUSG00000025900.10|OTTM... 3047 2802.580 \n", + "ENSMUST00000027032.5|ENSMUSG00000025900.10|OTTM... 6869 6624.580 \n", + "ENSMUST00000027035.9|ENSMUSG00000025902.13|OTTM... 3127 2882.580 \n", + "ENSMUST00000195555.1|ENSMUSG00000025902.13|OTTM... 1977 1732.580 \n", + "ENSMUST00000192650.5|ENSMUSG00000025902.13|OTTM... 3242 2997.580 \n", + "ENSMUST00000116652.7|ENSMUSG00000025902.13|OTTM... 1512 1267.580 \n", + "ENSMUST00000191647.1|ENSMUSG00000025902.13|OTTM... 406 163.270 \n", + "ENSMUST00000191939.1|ENSMUSG00000025902.13|OTTM... 840 595.579 \n", + "ENSMUST00000192913.1|ENSMUSG00000025902.13|OTTM... 1506 1261.580 \n", + "ENSMUST00000130201.7|ENSMUSG00000033845.13|OTTM... 1894 1649.580 \n", + "ENSMUST00000156816.6|ENSMUSG00000033845.13|OTTM... 4203 3958.580 \n", + "ENSMUST00000045689.13|ENSMUSG00000033845.13|OTT... 497 252.804 \n", + "ENSMUST00000146665.2|ENSMUSG00000033845.13|OTTM... 1569 1324.580 \n", + "ENSMUST00000134384.7|ENSMUSG00000025903.14|OTTM... 1136 891.579 \n", + "ENSMUST00000027036.10|ENSMUSG00000025903.14|OTT... 2507 2262.580 \n", + "ENSMUST00000150971.7|ENSMUSG00000025903.14|OTTM... 877 632.579 \n", + "\n", + " est_counts tpm \n", + "target_id \n", + "ENSMUST00000070533.4|ENSMUSG00000051951.5|OTTMU... 0.00000 0.000000 \n", + "ENSMUST00000194992.5|ENSMUSG00000025900.10|OTTM... 0.00000 0.000000 \n", + "ENSMUST00000027032.5|ENSMUSG00000025900.10|OTTM... 0.00000 0.000000 \n", + "ENSMUST00000027035.9|ENSMUSG00000025902.13|OTTM... 0.00000 0.000000 \n", + "ENSMUST00000195555.1|ENSMUSG00000025902.13|OTTM... 0.00000 0.000000 \n", + "ENSMUST00000192650.5|ENSMUSG00000025902.13|OTTM... 0.00000 0.000000 \n", + "ENSMUST00000116652.7|ENSMUSG00000025902.13|OTTM... 0.00000 0.000000 \n", + "ENSMUST00000191647.1|ENSMUSG00000025902.13|OTTM... 0.00000 0.000000 \n", + "ENSMUST00000191939.1|ENSMUSG00000025902.13|OTTM... 0.00000 0.000000 \n", + "ENSMUST00000192913.1|ENSMUSG00000025902.13|OTTM... 0.00000 0.000000 \n", + "ENSMUST00000130201.7|ENSMUSG00000033845.13|OTTM... 10.00000 0.212263 \n", + "ENSMUST00000156816.6|ENSMUSG00000033845.13|OTTM... 0.00000 0.000000 \n", + "ENSMUST00000045689.13|ENSMUSG00000033845.13|OTT... 0.00000 0.000000 \n", + "ENSMUST00000146665.2|ENSMUSG00000033845.13|OTTM... 0.00000 0.000000 \n", + "ENSMUST00000134384.7|ENSMUSG00000025903.14|OTTM... 5.42556 0.213075 \n", + "ENSMUST00000027036.10|ENSMUSG00000025903.14|OTT... 518.90900 8.030360 \n", + "ENSMUST00000150971.7|ENSMUSG00000025903.14|OTTM... 0.00000 0.000000 " + ] + }, + "execution_count": 37, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ - "# YOUR CODE HERE" + "# YOUR CODE HERE\n", + "s10_kallisto.head(17)" ] }, { "cell_type": "code", - "execution_count": null, + "execution_count": 38, "metadata": { "collapsed": false, "deletable": false, @@ -258,7 +637,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 39, "metadata": { "collapsed": false, "deletable": false, @@ -270,9 +649,20 @@ "solution": false } }, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "(56504, 4)" + ] + }, + "execution_count": 39, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ - "s13_kallisto.shape" + "s10_kallisto.shape" ] }, { @@ -295,7 +685,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 40, "metadata": { "collapsed": false, "deletable": false, @@ -307,7 +697,91 @@ "solution": false } }, - "outputs": [], + "outputs": [ + { + "data": { + "text/html": [ + "
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lengtheff_lengthest_countstpm
target_id
ENSMUST00000070533.4|ENSMUSG00000051951.5|OTTMUSG00000026353.2|OTTMUST00000065166.1|Xkr4-001|Xkr4|3634|UTR5:1-150|CDS:151-2094|UTR3:2095-3634|36343395.2420.03967
ENSMUST00000194992.5|ENSMUSG00000025900.10|OTTMUSG00000049985.2|OTTMUST00000127194.1|Rp1-002|Rp1|3047|UTR5:1-54|CDS:55-912|UTR3:913-3047|30472808.2400.00000
ENSMUST00000027032.5|ENSMUSG00000025900.10|OTTMUSG00000049985.2|OTTMUST00000127195.2|Rp1-001|Rp1|6869|UTR5:1-127|CDS:128-6415|UTR3:6416-6869|68696630.2400.00000
ENSMUST00000027035.9|ENSMUSG00000025902.13|OTTMUSG00000050014.7|OTTMUST00000127245.2|Sox17-001|Sox17|3127|UTR5:1-1082|CDS:1083-2342|UTR3:2343-3127|31272888.2400.00000
ENSMUST00000195555.1|ENSMUSG00000025902.13|OTTMUSG00000050014.7|OTTMUST00000127249.1|Sox17-005|Sox17|1977|UTR5:1-635|CDS:636-1511|UTR3:1512-1977|19771738.2400.00000
\n", + "
" + ], + "text/plain": [ + " length eff_length \\\n", + "target_id \n", + "ENSMUST00000070533.4|ENSMUSG00000051951.5|OTTMU... 3634 3395.24 \n", + "ENSMUST00000194992.5|ENSMUSG00000025900.10|OTTM... 3047 2808.24 \n", + "ENSMUST00000027032.5|ENSMUSG00000025900.10|OTTM... 6869 6630.24 \n", + "ENSMUST00000027035.9|ENSMUSG00000025902.13|OTTM... 3127 2888.24 \n", + "ENSMUST00000195555.1|ENSMUSG00000025902.13|OTTM... 1977 1738.24 \n", + "\n", + " est_counts tpm \n", + "target_id \n", + "ENSMUST00000070533.4|ENSMUSG00000051951.5|OTTMU... 2 0.03967 \n", + "ENSMUST00000194992.5|ENSMUSG00000025900.10|OTTM... 0 0.00000 \n", + "ENSMUST00000027032.5|ENSMUSG00000025900.10|OTTM... 0 0.00000 \n", + "ENSMUST00000027035.9|ENSMUSG00000025902.13|OTTM... 0 0.00000 \n", + "ENSMUST00000195555.1|ENSMUSG00000025902.13|OTTM... 0 0.00000 " + ] + }, + "execution_count": 40, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "s13_kallisto = pd.read_table('S13_kallisto/abundance.tsv', index_col='target_id')\n", "s13_kallisto.head()" @@ -333,7 +807,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 41, "metadata": { "collapsed": false, "deletable": false, @@ -345,14 +819,26 @@ "solution": true } }, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "(56504, 4)" + ] + }, + "execution_count": 41, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ - "# YOUR CODE HERE" + "# YOUR CODE HERE\n", + "s13_kallisto.shape" ] }, { "cell_type": "code", - "execution_count": null, + "execution_count": 42, "metadata": { "collapsed": false, "deletable": false, @@ -390,7 +876,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 43, "metadata": { "collapsed": false, "deletable": false, @@ -403,7 +889,36 @@ }, "scrolled": false }, - "outputs": [], + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/home/ucsd-train12/anaconda3/lib/python3.5/site-packages/matplotlib/__init__.py:892: UserWarning: axes.color_cycle is deprecated and replaced with axes.prop_cycle; please use the latter.\n", + " warnings.warn(self.msg_depr % (key, alt_key))\n" + ] + }, + { + "data": { + "text/plain": [ + "" + ] + }, + "execution_count": 43, + "metadata": {}, + "output_type": "execute_result" + }, + { + "data": { + "image/png": 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+ "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], "source": [ "sns.jointplot(s10_kallisto['tpm'], s13_kallisto['tpm'])" ] @@ -432,7 +947,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 44, "metadata": { "collapsed": false, "deletable": false, @@ -444,9 +959,100 @@ "solution": false } }, - "outputs": [], - "source": [ - "s10_kallisto['log2_tpm1000'] = np.log2(s10_kallisto['tpm']+10000)\n", + "outputs": [ + { + "data": { + "text/html": [ + "
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lengtheff_lengthest_countstpmlog2_tpm
target_id
ENSMUST00000070533.4|ENSMUSG00000051951.5|OTTMUSG00000026353.2|OTTMUST00000065166.1|Xkr4-001|Xkr4|3634|UTR5:1-150|CDS:151-2094|UTR3:2095-3634|36343389.58000
ENSMUST00000194992.5|ENSMUSG00000025900.10|OTTMUSG00000049985.2|OTTMUST00000127194.1|Rp1-002|Rp1|3047|UTR5:1-54|CDS:55-912|UTR3:913-3047|30472802.58000
ENSMUST00000027032.5|ENSMUSG00000025900.10|OTTMUSG00000049985.2|OTTMUST00000127195.2|Rp1-001|Rp1|6869|UTR5:1-127|CDS:128-6415|UTR3:6416-6869|68696624.58000
ENSMUST00000027035.9|ENSMUSG00000025902.13|OTTMUSG00000050014.7|OTTMUST00000127245.2|Sox17-001|Sox17|3127|UTR5:1-1082|CDS:1083-2342|UTR3:2343-3127|31272882.58000
ENSMUST00000195555.1|ENSMUSG00000025902.13|OTTMUSG00000050014.7|OTTMUST00000127249.1|Sox17-005|Sox17|1977|UTR5:1-635|CDS:636-1511|UTR3:1512-1977|19771732.58000
\n", + "
" + ], + "text/plain": [ + " length eff_length \\\n", + "target_id \n", + "ENSMUST00000070533.4|ENSMUSG00000051951.5|OTTMU... 3634 3389.58 \n", + "ENSMUST00000194992.5|ENSMUSG00000025900.10|OTTM... 3047 2802.58 \n", + "ENSMUST00000027032.5|ENSMUSG00000025900.10|OTTM... 6869 6624.58 \n", + "ENSMUST00000027035.9|ENSMUSG00000025902.13|OTTM... 3127 2882.58 \n", + "ENSMUST00000195555.1|ENSMUSG00000025902.13|OTTM... 1977 1732.58 \n", + "\n", + " est_counts tpm log2_tpm \n", + "target_id \n", + "ENSMUST00000070533.4|ENSMUSG00000051951.5|OTTMU... 0 0 0 \n", + "ENSMUST00000194992.5|ENSMUSG00000025900.10|OTTM... 0 0 0 \n", + "ENSMUST00000027032.5|ENSMUSG00000025900.10|OTTM... 0 0 0 \n", + "ENSMUST00000027035.9|ENSMUSG00000025902.13|OTTM... 0 0 0 \n", + "ENSMUST00000195555.1|ENSMUSG00000025902.13|OTTM... 0 0 0 " + ] + }, + "execution_count": 44, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "s10_kallisto['log2_tpm'] = np.log2(s10_kallisto['tpm']+1)\n", "s10_kallisto.head()" ] }, @@ -468,7 +1074,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 45, "metadata": { "collapsed": false, "deletable": false, @@ -481,16 +1087,115 @@ }, "scrolled": true }, - "outputs": [], + "outputs": [ + { + "data": { + "text/html": [ + "
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lengtheff_lengthest_countstpmlog2_tpm
target_id
ENSMUST00000070533.4|ENSMUSG00000051951.5|OTTMUSG00000026353.2|OTTMUST00000065166.1|Xkr4-001|Xkr4|3634|UTR5:1-150|CDS:151-2094|UTR3:2095-3634|36343395.2420.039670.056126
ENSMUST00000194992.5|ENSMUSG00000025900.10|OTTMUSG00000049985.2|OTTMUST00000127194.1|Rp1-002|Rp1|3047|UTR5:1-54|CDS:55-912|UTR3:913-3047|30472808.2400.000000.000000
ENSMUST00000027032.5|ENSMUSG00000025900.10|OTTMUSG00000049985.2|OTTMUST00000127195.2|Rp1-001|Rp1|6869|UTR5:1-127|CDS:128-6415|UTR3:6416-6869|68696630.2400.000000.000000
ENSMUST00000027035.9|ENSMUSG00000025902.13|OTTMUSG00000050014.7|OTTMUST00000127245.2|Sox17-001|Sox17|3127|UTR5:1-1082|CDS:1083-2342|UTR3:2343-3127|31272888.2400.000000.000000
ENSMUST00000195555.1|ENSMUSG00000025902.13|OTTMUSG00000050014.7|OTTMUST00000127249.1|Sox17-005|Sox17|1977|UTR5:1-635|CDS:636-1511|UTR3:1512-1977|19771738.2400.000000.000000
\n", + "
" + ], + "text/plain": [ + " length eff_length \\\n", + "target_id \n", + "ENSMUST00000070533.4|ENSMUSG00000051951.5|OTTMU... 3634 3395.24 \n", + "ENSMUST00000194992.5|ENSMUSG00000025900.10|OTTM... 3047 2808.24 \n", + "ENSMUST00000027032.5|ENSMUSG00000025900.10|OTTM... 6869 6630.24 \n", + "ENSMUST00000027035.9|ENSMUSG00000025902.13|OTTM... 3127 2888.24 \n", + "ENSMUST00000195555.1|ENSMUSG00000025902.13|OTTM... 1977 1738.24 \n", + "\n", + " est_counts tpm \\\n", + "target_id \n", + "ENSMUST00000070533.4|ENSMUSG00000051951.5|OTTMU... 2 0.03967 \n", + "ENSMUST00000194992.5|ENSMUSG00000025900.10|OTTM... 0 0.00000 \n", + "ENSMUST00000027032.5|ENSMUSG00000025900.10|OTTM... 0 0.00000 \n", + "ENSMUST00000027035.9|ENSMUSG00000025902.13|OTTM... 0 0.00000 \n", + "ENSMUST00000195555.1|ENSMUSG00000025902.13|OTTM... 0 0.00000 \n", + "\n", + " log2_tpm \n", + "target_id \n", + "ENSMUST00000070533.4|ENSMUSG00000051951.5|OTTMU... 0.056126 \n", + "ENSMUST00000194992.5|ENSMUSG00000025900.10|OTTM... 0.000000 \n", + "ENSMUST00000027032.5|ENSMUSG00000025900.10|OTTM... 0.000000 \n", + "ENSMUST00000027035.9|ENSMUSG00000025902.13|OTTM... 0.000000 \n", + "ENSMUST00000195555.1|ENSMUSG00000025902.13|OTTM... 0.000000 " + ] + }, + "execution_count": 45, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "# YOUR CODE HERE\n", - "\n", + "s13_kallisto['log2_tpm'] = np.log2(s13_kallisto['tpm']+1)\n", "s13_kallisto.head()" ] }, { "cell_type": "code", - "execution_count": null, + "execution_count": 46, "metadata": { "collapsed": false, "deletable": false, @@ -529,7 +1234,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 47, "metadata": { "collapsed": false, "deletable": false, @@ -541,14 +1246,44 @@ "solution": true } }, - "outputs": [], + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/home/ucsd-train12/anaconda3/lib/python3.5/site-packages/matplotlib/__init__.py:892: UserWarning: axes.color_cycle is deprecated and replaced with axes.prop_cycle; please use the latter.\n", + " warnings.warn(self.msg_depr % (key, alt_key))\n" + ] + }, + { + "data": { + "text/plain": [ + "" + ] + }, + "execution_count": 47, + "metadata": {}, + "output_type": "execute_result" + }, + { + "data": { + "image/png": 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aew8NYc29VzKcaNJY/EBURKWuTkv3eiNuH1Zt6MY9q7cU5Nwi7WsNjni41xYVBHtMREVU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\nDe3F7D98Aq/v7oPVkrwRs9mkxHshpep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+ "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], "source": [ - "# YOUR CODE HERE" + "# YOUR CODE HERE\n", + "sns.jointplot(s10_kallisto['log2_tpm'], s13_kallisto['log2_tpm'])" ] }, { "cell_type": "code", - "execution_count": null, + "execution_count": 48, "metadata": { "collapsed": true, "deletable": false, @@ -584,7 +1319,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 49, "metadata": { "collapsed": false, "deletable": false, @@ -596,7 +1331,36 @@ "solution": false } }, - "outputs": [], + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/home/ucsd-train12/anaconda3/lib/python3.5/site-packages/matplotlib/__init__.py:892: UserWarning: axes.color_cycle is deprecated and replaced with axes.prop_cycle; please use the latter.\n", + " warnings.warn(self.msg_depr % (key, alt_key))\n" + ] + }, + { + "data": { + "text/plain": [ + "" + ] + }, + "execution_count": 49, + "metadata": {}, + "output_type": "execute_result" + }, + { + "data": { + "image/png": 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4LJjToigFzyf1ibQOuyWpGs9kAk6bOSXl7r+J5y89de/lWPnsW4oAT/e5pvtB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\nNjoQRhhdu/oUJ9MGQ8Ca9d24Ycl8PLj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+ "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], "source": [ "from scipy.stats import spearmanr\n", "\n", @@ -621,7 +1385,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 50, "metadata": { "collapsed": false, "deletable": false, @@ -633,7 +1397,69 @@ "solution": false } }, - "outputs": [], + "outputs": [ + { + "data": { + "text/html": [ + "
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s10s13
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ENSMUST00000027035.9|ENSMUSG00000025902.13|OTTMUSG00000050014.7|OTTMUST00000127245.2|Sox17-001|Sox17|3127|UTR5:1-1082|CDS:1083-2342|UTR3:2343-3127|00.000000
ENSMUST00000195555.1|ENSMUSG00000025902.13|OTTMUSG00000050014.7|OTTMUST00000127249.1|Sox17-005|Sox17|1977|UTR5:1-635|CDS:636-1511|UTR3:1512-1977|00.000000
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" + ], + "text/plain": [ + " s10 s13\n", + "target_id \n", + "ENSMUST00000070533.4|ENSMUSG00000051951.5|OTTMU... 0 0.056126\n", + "ENSMUST00000194992.5|ENSMUSG00000025900.10|OTTM... 0 0.000000\n", + "ENSMUST00000027032.5|ENSMUSG00000025900.10|OTTM... 0 0.000000\n", + "ENSMUST00000027035.9|ENSMUSG00000025902.13|OTTM... 0 0.000000\n", + "ENSMUST00000195555.1|ENSMUSG00000025902.13|OTTM... 0 0.000000" + ] + }, + "execution_count": 50, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "kallisto_log2_tpm = pd.concat([s10_kallisto['log2_tpm'], s13_kallisto['log2_tpm']], axis=1, keys=['s10', 's13'])\n", "kallisto_log2_tpm.head()" @@ -657,7 +1483,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 51, "metadata": { "collapsed": false, "deletable": false, @@ -669,7 +1495,408 @@ "solution": false } }, - "outputs": [], + "outputs": [ + { + "data": { + "text/html": [ + "
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s10s13
target_id
ENSMUST00000070533.4|ENSMUSG00000051951.5|OTTMUSG00000026353.2|OTTMUST00000065166.1|Xkr4-001|Xkr4|3634|UTR5:1-150|CDS:151-2094|UTR3:2095-3634|FalseFalse
ENSMUST00000194992.5|ENSMUSG00000025900.10|OTTMUSG00000049985.2|OTTMUST00000127194.1|Rp1-002|Rp1|3047|UTR5:1-54|CDS:55-912|UTR3:913-3047|FalseFalse
ENSMUST00000027032.5|ENSMUSG00000025900.10|OTTMUSG00000049985.2|OTTMUST00000127195.2|Rp1-001|Rp1|6869|UTR5:1-127|CDS:128-6415|UTR3:6416-6869|FalseFalse
ENSMUST00000027035.9|ENSMUSG00000025902.13|OTTMUSG00000050014.7|OTTMUST00000127245.2|Sox17-001|Sox17|3127|UTR5:1-1082|CDS:1083-2342|UTR3:2343-3127|FalseFalse
ENSMUST00000195555.1|ENSMUSG00000025902.13|OTTMUSG00000050014.7|OTTMUST00000127249.1|Sox17-005|Sox17|1977|UTR5:1-635|CDS:636-1511|UTR3:1512-1977|FalseFalse
ENSMUST00000192650.5|ENSMUSG00000025902.13|OTTMUSG00000050014.7|OTTMUST00000127247.2|Sox17-004|Sox17|3242|UTR5:1-1851|CDS:1852-2916|UTR3:2917-3242|FalseFalse
ENSMUST00000116652.7|ENSMUSG00000025902.13|OTTMUSG00000050014.7|OTTMUST00000127246.1|Sox17-002|Sox17|1512|UTR5:1-249|CDS:250-1509|UTR3:1510-1512|FalseFalse
ENSMUST00000191647.1|ENSMUSG00000025902.13|OTTMUSG00000050014.7|OTTMUST00000127267.2|Sox17-007|Sox17|406|UTR5:1-83|CDS:84-406|FalseFalse
ENSMUST00000191939.1|ENSMUSG00000025902.13|OTTMUSG00000050014.7|OTTMUST00000127266.2|Sox17-006|Sox17|840|UTR5:1-329|CDS:330-840|FalseFalse
ENSMUST00000192913.1|ENSMUSG00000025902.13|OTTMUSG00000050014.7|OTTMUST00000127248.2|Sox17-003|Sox17|1506|UTR5:1-997|CDS:998-1506|FalseFalse
ENSMUST00000130201.7|ENSMUSG00000033845.13|OTTMUSG00000029329.3|OTTMUST00000072660.1|Mrpl15-002|Mrpl15|1894|UTR5:1-33|CDS:34-648|UTR3:649-1894|FalseFalse
ENSMUST00000156816.6|ENSMUSG00000033845.13|OTTMUSG00000029329.3|OTTMUST00000072659.1|Mrpl15-001|Mrpl15|4203|UTR5:1-62|CDS:63-950|UTR3:951-4203|FalseFalse
ENSMUST00000045689.13|ENSMUSG00000033845.13|OTTMUSG00000029329.3|OTTMUST00000072661.1|Mrpl15-003|Mrpl15|497|UTR5:1-21|CDS:22-180|UTR3:181-497|FalseFalse
ENSMUST00000146665.2|ENSMUSG00000033845.13|OTTMUSG00000029329.3|OTTMUST00000072662.2|Mrpl15-004|Mrpl15|1569|UTR5:1-62|CDS:63-569|UTR3:570-1569|FalseTrue
ENSMUST00000134384.7|ENSMUSG00000025903.14|OTTMUSG00000021562.4|OTTMUST00000051163.2|Lypla1-002|Lypla1|1136|UTR5:1-126|CDS:127-801|UTR3:802-1136|FalseTrue
ENSMUST00000027036.10|ENSMUSG00000025903.14|OTTMUSG00000021562.4|OTTMUST00000051162.1|Lypla1-001|Lypla1|2507|UTR5:1-91|CDS:92-784|UTR3:785-2507|TrueTrue
ENSMUST00000150971.7|ENSMUSG00000025903.14|OTTMUSG00000021562.4|OTTMUST00000051164.3|Lypla1-003|Lypla1|877|UTR5:1-84|CDS:85-750|UTR3:751-877|FalseFalse
ENSMUST00000119612.8|ENSMUSG00000025903.14|OTTMUSG00000021562.4|OTTMUST00000051170.2|Lypla1-009|Lypla1|529|UTR5:1-18|CDS:19-297|UTR3:298-529|FalseFalse
ENSMUST00000137887.7|ENSMUSG00000025903.14|OTTMUSG00000021562.4|OTTMUST00000051168.2|Lypla1-007|Lypla1|444|UTR5:1-16|CDS:17-444|FalseFalse
ENSMUST00000115529.7|ENSMUSG00000025903.14|OTTMUSG00000021562.4|OTTMUST00000051169.1|Lypla1-008|Lypla1|930|UTR5:1-3|CDS:4-594|UTR3:595-930|FalseFalse
ENSMUST00000131119.1|ENSMUSG00000025903.14|OTTMUSG00000021562.4|OTTMUST00000051167.3|Lypla1-006|Lypla1|660|UTR5:1-234|CDS:235-660|FalseFalse
ENSMUST00000155020.1|ENSMUSG00000104217.1|OTTMUSG00000050100.1|OTTMUST00000127419.1|Gm37988-001|Gm37988|825|UTR5:1-22|CDS:23-211|UTR3:212-825|FalseFalse
ENSMUST00000081551.13|ENSMUSG00000033813.15|OTTMUSG00000042348.1|OTTMUST00000111602.1|Tcea1-001|Tcea1|2547|UTR5:1-100|CDS:101-1006|UTR3:1007-2547|TrueTrue
ENSMUST00000165720.2|ENSMUSG00000033813.15|OTTMUSG00000042348.1|OTTMUST00000111603.1|Tcea1-002|Tcea1|2854|UTR5:1-370|CDS:371-1309|UTR3:1310-2854|FalseFalse
ENSMUST00000002533.14|ENSMUSG00000002459.17|OTTMUSG00000029338.4|OTTMUST00000072687.1|Rgs20-002|Rgs20|1778|UTR5:1-160|CDS:161-880|UTR3:881-1778|TrueTrue
ENSMUST00000118000.7|ENSMUSG00000002459.17|OTTMUSG00000029338.4|OTTMUST00000072688.2|Rgs20-001|Rgs20|2125|UTR5:1-108|CDS:109-1227|UTR3:1228-2125|FalseFalse
ENSMUST00000119256.7|ENSMUSG00000002459.17|OTTMUSG00000029338.4|OTTMUST00000072706.2|Rgs20-005|Rgs20|883|UTR5:1-184|CDS:185-811|UTR3:812-883|FalseFalse
ENSMUST00000170566.1|ENSMUSG00000002459.17|OTTMUSG00000029338.4|OTTMUST00000092053.1|Rgs20-007|Rgs20|577|CDS:1-120|UTR3:121-577|FalseFalse
ENSMUST00000147158.1|ENSMUSG00000002459.17|OTTMUSG00000029338.4|OTTMUST00000072705.2|Rgs20-004|Rgs20|707|UTR5:1-105|CDS:106-707|FalseFalse
ENSMUST00000192847.5|ENSMUSG00000033793.12|OTTMUSG00000050145.9|OTTMUST00000127492.1|Atp6v1h-003|Atp6v1h|1662|UTR5:1-161|CDS:162-1487|UTR3:1488-1662|TrueFalse
.........
ENSMUST00000178889.1|ENSMUSG00000095650.2|OTTMUSG00000042966.1|-|Gm20854-201|Gm20854|1002|UTR5:1-175|CDS:176-859|UTR3:860-1002|FalseFalse
ENSMUST00000181549.1|ENSMUSG00000095650.2|OTTMUSG00000042966.1|OTTMUST00000112802.1|Gm20854-001|Gm20854|1156|UTR5:1-335|CDS:336-1019|UTR3:1020-1156|FalseFalse
ENSMUST00000188754.1|ENSMUSG00000100240.1|OTTMUSG00000047031.1|OTTMUST00000121805.1|Gm20820-001|Gm20820|921|UTR5:1-58|CDS:59-727|UTR3:728-921|FalseFalse
ENSMUST00000189543.6|ENSMUSG00000094399.7|OTTMUSG00000047083.1|OTTMUST00000121876.1|Gm21477-001|Gm21477|924|UTR5:1-58|CDS:59-727|UTR3:728-924|FalseFalse
ENSMUST00000179970.1|ENSMUSG00000094399.7|OTTMUSG00000047083.1|-|Gm21477-201|Gm21477|498|CDS:1-498|FalseFalse
ENSMUST00000186493.1|ENSMUSG00000099856.1|OTTMUSG00000047138.1|OTTMUST00000121968.1|Gm20906-001|Gm20906|923|UTR5:1-58|CDS:59-727|UTR3:728-923|FalseFalse
ENSMUST00000187146.1|ENSMUSG00000101915.1|OTTMUSG00000047149.1|OTTMUST00000121980.1|Gm28102-001|Gm28102|924|UTR5:1-58|CDS:59-727|UTR3:728-924|FalseFalse
ENSMUST00000186443.1|ENSMUSG00000102045.1|OTTMUSG00000047309.1|OTTMUST00000122306.1|Gm21294-001|Gm21294|934|UTR5:1-73|CDS:74-742|UTR3:743-934|FalseFalse
ENSMUST00000188269.1|ENSMUSG00000100608.1|OTTMUSG00000047316.1|OTTMUST00000122318.1|Gm21996-001|Gm21996|931|UTR5:1-58|CDS:59-727|UTR3:728-931|FalseFalse
ENSMUST00000190558.6|ENSMUSG00000096178.7|OTTMUSG00000047352.1|OTTMUST00000122361.1|Gm20837-001|Gm20837|844|UTR5:1-73|CDS:74-640|UTR3:641-844|FalseFalse
ENSMUST00000178446.1|ENSMUSG00000096178.7|OTTMUSG00000047352.1|-|Gm20837-201|Gm20837|498|CDS:1-498|FalseFalse
ENSMUST00000177893.1|ENSMUSG00000095366.1|-|-|Gm21860-201|Gm21860|309|CDS:1-309|FalseFalse
ENSMUST00000179483.7|ENSMUSG00000096768.7|-|-|Erdr1-204|Erdr1|688|UTR5:1-70|CDS:71-688|FalseFalse
ENSMUST00000177591.1|ENSMUSG00000096768.7|-|-|Erdr1-201|Erdr1|774|UTR5:1-229|CDS:230-757|UTR3:758-774|FalseFalse
ENSMUST00000177671.7|ENSMUSG00000096768.7|-|-|Erdr1-202|Erdr1|708|UTR5:1-159|CDS:160-528|UTR3:529-708|FalseFalse
ENSMUST00000179077.1|ENSMUSG00000096768.7|-|-|Erdr1-203|Erdr1|887|UTR5:1-74|CDS:75-512|UTR3:513-887|FalseFalse
ENSMUST00000179623.1|ENSMUSG00000096850.1|-|-|Gm21748-201|Gm21748|309|CDS:1-309|FalseFalse
ENSMUST00000082392.1|ENSMUSG00000064341.1|-|-|mt-Nd1-201|mt-Nd1|957|CDS:1-957|TrueTrue
ENSMUST00000082396.1|ENSMUSG00000064345.1|-|-|mt-Nd2-201|mt-Nd2|1038|CDS:1-1038|TrueTrue
ENSMUST00000082402.1|ENSMUSG00000064351.1|-|-|mt-Co1-201|mt-Co1|1545|CDS:1-1545|TrueTrue
ENSMUST00000082405.1|ENSMUSG00000064354.1|-|-|mt-Co2-201|mt-Co2|684|CDS:1-684|TrueTrue
ENSMUST00000082407.1|ENSMUSG00000064356.3|-|-|mt-Atp8-201|mt-Atp8|204|CDS:1-204|TrueTrue
ENSMUST00000082408.1|ENSMUSG00000064357.1|-|-|mt-Atp6-201|mt-Atp6|681|CDS:1-681|TrueTrue
ENSMUST00000082409.1|ENSMUSG00000064358.1|-|-|mt-Co3-201|mt-Co3|784|CDS:1-784|TrueTrue
ENSMUST00000082411.1|ENSMUSG00000064360.1|-|-|mt-Nd3-201|mt-Nd3|348|CDS:1-348|TrueTrue
ENSMUST00000084013.1|ENSMUSG00000065947.3|-|-|mt-Nd4l-201|mt-Nd4l|297|CDS:1-297|TrueTrue
ENSMUST00000082414.1|ENSMUSG00000064363.1|-|-|mt-Nd4-201|mt-Nd4|1378|CDS:1-1378|TrueTrue
ENSMUST00000082418.1|ENSMUSG00000064367.1|-|-|mt-Nd5-201|mt-Nd5|1824|CDS:1-1824|TrueTrue
ENSMUST00000082419.1|ENSMUSG00000064368.1|-|-|mt-Nd6-201|mt-Nd6|519|CDS:1-519|TrueTrue
ENSMUST00000082421.1|ENSMUSG00000064370.1|-|-|mt-Cytb-201|mt-Cytb|1144|CDS:1-1144|TrueTrue
\n", + "

56504 rows × 2 columns

\n", + "
" + ], + "text/plain": [ + " s10 s13\n", + "target_id \n", + "ENSMUST00000070533.4|ENSMUSG00000051951.5|OTTMU... False False\n", + "ENSMUST00000194992.5|ENSMUSG00000025900.10|OTTM... False False\n", + "ENSMUST00000027032.5|ENSMUSG00000025900.10|OTTM... False False\n", + "ENSMUST00000027035.9|ENSMUSG00000025902.13|OTTM... False False\n", + "ENSMUST00000195555.1|ENSMUSG00000025902.13|OTTM... False False\n", + "ENSMUST00000192650.5|ENSMUSG00000025902.13|OTTM... False False\n", + "ENSMUST00000116652.7|ENSMUSG00000025902.13|OTTM... False False\n", + "ENSMUST00000191647.1|ENSMUSG00000025902.13|OTTM... False False\n", + "ENSMUST00000191939.1|ENSMUSG00000025902.13|OTTM... False False\n", + "ENSMUST00000192913.1|ENSMUSG00000025902.13|OTTM... False False\n", + "ENSMUST00000130201.7|ENSMUSG00000033845.13|OTTM... False False\n", + "ENSMUST00000156816.6|ENSMUSG00000033845.13|OTTM... False False\n", + "ENSMUST00000045689.13|ENSMUSG00000033845.13|OTT... False False\n", + "ENSMUST00000146665.2|ENSMUSG00000033845.13|OTTM... False True\n", + "ENSMUST00000134384.7|ENSMUSG00000025903.14|OTTM... False True\n", + "ENSMUST00000027036.10|ENSMUSG00000025903.14|OTT... True True\n", + "ENSMUST00000150971.7|ENSMUSG00000025903.14|OTTM... False False\n", + "ENSMUST00000119612.8|ENSMUSG00000025903.14|OTTM... False False\n", + "ENSMUST00000137887.7|ENSMUSG00000025903.14|OTTM... False False\n", + "ENSMUST00000115529.7|ENSMUSG00000025903.14|OTTM... False False\n", + "ENSMUST00000131119.1|ENSMUSG00000025903.14|OTTM... False False\n", + "ENSMUST00000155020.1|ENSMUSG00000104217.1|OTTMU... False False\n", + "ENSMUST00000081551.13|ENSMUSG00000033813.15|OTT... True True\n", + "ENSMUST00000165720.2|ENSMUSG00000033813.15|OTTM... False False\n", + "ENSMUST00000002533.14|ENSMUSG00000002459.17|OTT... True True\n", + "ENSMUST00000118000.7|ENSMUSG00000002459.17|OTTM... False False\n", + "ENSMUST00000119256.7|ENSMUSG00000002459.17|OTTM... False False\n", + "ENSMUST00000170566.1|ENSMUSG00000002459.17|OTTM... False False\n", + "ENSMUST00000147158.1|ENSMUSG00000002459.17|OTTM... False False\n", + "ENSMUST00000192847.5|ENSMUSG00000033793.12|OTTM... True False\n", + "... ... ...\n", + "ENSMUST00000178889.1|ENSMUSG00000095650.2|OTTMU... False False\n", + "ENSMUST00000181549.1|ENSMUSG00000095650.2|OTTMU... False False\n", + "ENSMUST00000188754.1|ENSMUSG00000100240.1|OTTMU... False False\n", + "ENSMUST00000189543.6|ENSMUSG00000094399.7|OTTMU... False False\n", + "ENSMUST00000179970.1|ENSMUSG00000094399.7|OTTMU... False False\n", + "ENSMUST00000186493.1|ENSMUSG00000099856.1|OTTMU... False False\n", + "ENSMUST00000187146.1|ENSMUSG00000101915.1|OTTMU... False False\n", + "ENSMUST00000186443.1|ENSMUSG00000102045.1|OTTMU... False False\n", + "ENSMUST00000188269.1|ENSMUSG00000100608.1|OTTMU... False False\n", + "ENSMUST00000190558.6|ENSMUSG00000096178.7|OTTMU... False False\n", + "ENSMUST00000178446.1|ENSMUSG00000096178.7|OTTMU... False False\n", + "ENSMUST00000177893.1|ENSMUSG00000095366.1|-|-|G... False False\n", + "ENSMUST00000179483.7|ENSMUSG00000096768.7|-|-|E... False False\n", + "ENSMUST00000177591.1|ENSMUSG00000096768.7|-|-|E... False False\n", + "ENSMUST00000177671.7|ENSMUSG00000096768.7|-|-|E... False False\n", + "ENSMUST00000179077.1|ENSMUSG00000096768.7|-|-|E... False False\n", + "ENSMUST00000179623.1|ENSMUSG00000096850.1|-|-|G... False False\n", + "ENSMUST00000082392.1|ENSMUSG00000064341.1|-|-|m... True True\n", + "ENSMUST00000082396.1|ENSMUSG00000064345.1|-|-|m... True True\n", + "ENSMUST00000082402.1|ENSMUSG00000064351.1|-|-|m... True True\n", + "ENSMUST00000082405.1|ENSMUSG00000064354.1|-|-|m... True True\n", + "ENSMUST00000082407.1|ENSMUSG00000064356.3|-|-|m... True True\n", + "ENSMUST00000082408.1|ENSMUSG00000064357.1|-|-|m... True True\n", + "ENSMUST00000082409.1|ENSMUSG00000064358.1|-|-|m... True True\n", + "ENSMUST00000082411.1|ENSMUSG00000064360.1|-|-|m... True True\n", + "ENSMUST00000084013.1|ENSMUSG00000065947.3|-|-|m... True True\n", + "ENSMUST00000082414.1|ENSMUSG00000064363.1|-|-|m... True True\n", + "ENSMUST00000082418.1|ENSMUSG00000064367.1|-|-|m... True True\n", + "ENSMUST00000082419.1|ENSMUSG00000064368.1|-|-|m... True True\n", + "ENSMUST00000082421.1|ENSMUSG00000064370.1|-|-|m... True True\n", + "\n", + "[56504 rows x 2 columns]" + ] + }, + "execution_count": 51, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "kallisto_log2_tpm > 1" ] @@ -692,7 +1919,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 52, "metadata": { "collapsed": false, "deletable": false, @@ -704,7 +1931,20 @@ "solution": false } }, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "s10 6121\n", + "s13 6380\n", + "dtype: int64" + ] + }, + "execution_count": 52, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "(kallisto_log2_tpm > 1).sum()" ] @@ -727,7 +1967,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 53, "metadata": { "collapsed": false, "deletable": false, @@ -739,7 +1979,80 @@ "solution": false } }, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "target_id\n", + "ENSMUST00000070533.4|ENSMUSG00000051951.5|OTTMUSG00000026353.2|OTTMUST00000065166.1|Xkr4-001|Xkr4|3634|UTR5:1-150|CDS:151-2094|UTR3:2095-3634| 0\n", + "ENSMUST00000194992.5|ENSMUSG00000025900.10|OTTMUSG00000049985.2|OTTMUST00000127194.1|Rp1-002|Rp1|3047|UTR5:1-54|CDS:55-912|UTR3:913-3047| 0\n", + "ENSMUST00000027032.5|ENSMUSG00000025900.10|OTTMUSG00000049985.2|OTTMUST00000127195.2|Rp1-001|Rp1|6869|UTR5:1-127|CDS:128-6415|UTR3:6416-6869| 0\n", + "ENSMUST00000027035.9|ENSMUSG00000025902.13|OTTMUSG00000050014.7|OTTMUST00000127245.2|Sox17-001|Sox17|3127|UTR5:1-1082|CDS:1083-2342|UTR3:2343-3127| 0\n", + "ENSMUST00000195555.1|ENSMUSG00000025902.13|OTTMUSG00000050014.7|OTTMUST00000127249.1|Sox17-005|Sox17|1977|UTR5:1-635|CDS:636-1511|UTR3:1512-1977| 0\n", + "ENSMUST00000192650.5|ENSMUSG00000025902.13|OTTMUSG00000050014.7|OTTMUST00000127247.2|Sox17-004|Sox17|3242|UTR5:1-1851|CDS:1852-2916|UTR3:2917-3242| 0\n", + "ENSMUST00000116652.7|ENSMUSG00000025902.13|OTTMUSG00000050014.7|OTTMUST00000127246.1|Sox17-002|Sox17|1512|UTR5:1-249|CDS:250-1509|UTR3:1510-1512| 0\n", + "ENSMUST00000191647.1|ENSMUSG00000025902.13|OTTMUSG00000050014.7|OTTMUST00000127267.2|Sox17-007|Sox17|406|UTR5:1-83|CDS:84-406| 0\n", + "ENSMUST00000191939.1|ENSMUSG00000025902.13|OTTMUSG00000050014.7|OTTMUST00000127266.2|Sox17-006|Sox17|840|UTR5:1-329|CDS:330-840| 0\n", + "ENSMUST00000192913.1|ENSMUSG00000025902.13|OTTMUSG00000050014.7|OTTMUST00000127248.2|Sox17-003|Sox17|1506|UTR5:1-997|CDS:998-1506| 0\n", + "ENSMUST00000130201.7|ENSMUSG00000033845.13|OTTMUSG00000029329.3|OTTMUST00000072660.1|Mrpl15-002|Mrpl15|1894|UTR5:1-33|CDS:34-648|UTR3:649-1894| 0\n", + "ENSMUST00000156816.6|ENSMUSG00000033845.13|OTTMUSG00000029329.3|OTTMUST00000072659.1|Mrpl15-001|Mrpl15|4203|UTR5:1-62|CDS:63-950|UTR3:951-4203| 0\n", + "ENSMUST00000045689.13|ENSMUSG00000033845.13|OTTMUSG00000029329.3|OTTMUST00000072661.1|Mrpl15-003|Mrpl15|497|UTR5:1-21|CDS:22-180|UTR3:181-497| 0\n", + "ENSMUST00000146665.2|ENSMUSG00000033845.13|OTTMUSG00000029329.3|OTTMUST00000072662.2|Mrpl15-004|Mrpl15|1569|UTR5:1-62|CDS:63-569|UTR3:570-1569| 1\n", + "ENSMUST00000134384.7|ENSMUSG00000025903.14|OTTMUSG00000021562.4|OTTMUST00000051163.2|Lypla1-002|Lypla1|1136|UTR5:1-126|CDS:127-801|UTR3:802-1136| 1\n", + "ENSMUST00000027036.10|ENSMUSG00000025903.14|OTTMUSG00000021562.4|OTTMUST00000051162.1|Lypla1-001|Lypla1|2507|UTR5:1-91|CDS:92-784|UTR3:785-2507| 2\n", + "ENSMUST00000150971.7|ENSMUSG00000025903.14|OTTMUSG00000021562.4|OTTMUST00000051164.3|Lypla1-003|Lypla1|877|UTR5:1-84|CDS:85-750|UTR3:751-877| 0\n", + "ENSMUST00000119612.8|ENSMUSG00000025903.14|OTTMUSG00000021562.4|OTTMUST00000051170.2|Lypla1-009|Lypla1|529|UTR5:1-18|CDS:19-297|UTR3:298-529| 0\n", + "ENSMUST00000137887.7|ENSMUSG00000025903.14|OTTMUSG00000021562.4|OTTMUST00000051168.2|Lypla1-007|Lypla1|444|UTR5:1-16|CDS:17-444| 0\n", + "ENSMUST00000115529.7|ENSMUSG00000025903.14|OTTMUSG00000021562.4|OTTMUST00000051169.1|Lypla1-008|Lypla1|930|UTR5:1-3|CDS:4-594|UTR3:595-930| 0\n", + "ENSMUST00000131119.1|ENSMUSG00000025903.14|OTTMUSG00000021562.4|OTTMUST00000051167.3|Lypla1-006|Lypla1|660|UTR5:1-234|CDS:235-660| 0\n", + "ENSMUST00000155020.1|ENSMUSG00000104217.1|OTTMUSG00000050100.1|OTTMUST00000127419.1|Gm37988-001|Gm37988|825|UTR5:1-22|CDS:23-211|UTR3:212-825| 0\n", + "ENSMUST00000081551.13|ENSMUSG00000033813.15|OTTMUSG00000042348.1|OTTMUST00000111602.1|Tcea1-001|Tcea1|2547|UTR5:1-100|CDS:101-1006|UTR3:1007-2547| 2\n", + "ENSMUST00000165720.2|ENSMUSG00000033813.15|OTTMUSG00000042348.1|OTTMUST00000111603.1|Tcea1-002|Tcea1|2854|UTR5:1-370|CDS:371-1309|UTR3:1310-2854| 0\n", + "ENSMUST00000002533.14|ENSMUSG00000002459.17|OTTMUSG00000029338.4|OTTMUST00000072687.1|Rgs20-002|Rgs20|1778|UTR5:1-160|CDS:161-880|UTR3:881-1778| 2\n", + "ENSMUST00000118000.7|ENSMUSG00000002459.17|OTTMUSG00000029338.4|OTTMUST00000072688.2|Rgs20-001|Rgs20|2125|UTR5:1-108|CDS:109-1227|UTR3:1228-2125| 0\n", + "ENSMUST00000119256.7|ENSMUSG00000002459.17|OTTMUSG00000029338.4|OTTMUST00000072706.2|Rgs20-005|Rgs20|883|UTR5:1-184|CDS:185-811|UTR3:812-883| 0\n", + "ENSMUST00000170566.1|ENSMUSG00000002459.17|OTTMUSG00000029338.4|OTTMUST00000092053.1|Rgs20-007|Rgs20|577|CDS:1-120|UTR3:121-577| 0\n", + "ENSMUST00000147158.1|ENSMUSG00000002459.17|OTTMUSG00000029338.4|OTTMUST00000072705.2|Rgs20-004|Rgs20|707|UTR5:1-105|CDS:106-707| 0\n", + "ENSMUST00000192847.5|ENSMUSG00000033793.12|OTTMUSG00000050145.9|OTTMUST00000127492.1|Atp6v1h-003|Atp6v1h|1662|UTR5:1-161|CDS:162-1487|UTR3:1488-1662| 1\n", + " ..\n", + "ENSMUST00000178889.1|ENSMUSG00000095650.2|OTTMUSG00000042966.1|-|Gm20854-201|Gm20854|1002|UTR5:1-175|CDS:176-859|UTR3:860-1002| 0\n", + "ENSMUST00000181549.1|ENSMUSG00000095650.2|OTTMUSG00000042966.1|OTTMUST00000112802.1|Gm20854-001|Gm20854|1156|UTR5:1-335|CDS:336-1019|UTR3:1020-1156| 0\n", + "ENSMUST00000188754.1|ENSMUSG00000100240.1|OTTMUSG00000047031.1|OTTMUST00000121805.1|Gm20820-001|Gm20820|921|UTR5:1-58|CDS:59-727|UTR3:728-921| 0\n", + "ENSMUST00000189543.6|ENSMUSG00000094399.7|OTTMUSG00000047083.1|OTTMUST00000121876.1|Gm21477-001|Gm21477|924|UTR5:1-58|CDS:59-727|UTR3:728-924| 0\n", + "ENSMUST00000179970.1|ENSMUSG00000094399.7|OTTMUSG00000047083.1|-|Gm21477-201|Gm21477|498|CDS:1-498| 0\n", + "ENSMUST00000186493.1|ENSMUSG00000099856.1|OTTMUSG00000047138.1|OTTMUST00000121968.1|Gm20906-001|Gm20906|923|UTR5:1-58|CDS:59-727|UTR3:728-923| 0\n", + "ENSMUST00000187146.1|ENSMUSG00000101915.1|OTTMUSG00000047149.1|OTTMUST00000121980.1|Gm28102-001|Gm28102|924|UTR5:1-58|CDS:59-727|UTR3:728-924| 0\n", + "ENSMUST00000186443.1|ENSMUSG00000102045.1|OTTMUSG00000047309.1|OTTMUST00000122306.1|Gm21294-001|Gm21294|934|UTR5:1-73|CDS:74-742|UTR3:743-934| 0\n", + "ENSMUST00000188269.1|ENSMUSG00000100608.1|OTTMUSG00000047316.1|OTTMUST00000122318.1|Gm21996-001|Gm21996|931|UTR5:1-58|CDS:59-727|UTR3:728-931| 0\n", + "ENSMUST00000190558.6|ENSMUSG00000096178.7|OTTMUSG00000047352.1|OTTMUST00000122361.1|Gm20837-001|Gm20837|844|UTR5:1-73|CDS:74-640|UTR3:641-844| 0\n", + "ENSMUST00000178446.1|ENSMUSG00000096178.7|OTTMUSG00000047352.1|-|Gm20837-201|Gm20837|498|CDS:1-498| 0\n", + "ENSMUST00000177893.1|ENSMUSG00000095366.1|-|-|Gm21860-201|Gm21860|309|CDS:1-309| 0\n", + "ENSMUST00000179483.7|ENSMUSG00000096768.7|-|-|Erdr1-204|Erdr1|688|UTR5:1-70|CDS:71-688| 0\n", + "ENSMUST00000177591.1|ENSMUSG00000096768.7|-|-|Erdr1-201|Erdr1|774|UTR5:1-229|CDS:230-757|UTR3:758-774| 0\n", + "ENSMUST00000177671.7|ENSMUSG00000096768.7|-|-|Erdr1-202|Erdr1|708|UTR5:1-159|CDS:160-528|UTR3:529-708| 0\n", + "ENSMUST00000179077.1|ENSMUSG00000096768.7|-|-|Erdr1-203|Erdr1|887|UTR5:1-74|CDS:75-512|UTR3:513-887| 0\n", + "ENSMUST00000179623.1|ENSMUSG00000096850.1|-|-|Gm21748-201|Gm21748|309|CDS:1-309| 0\n", + "ENSMUST00000082392.1|ENSMUSG00000064341.1|-|-|mt-Nd1-201|mt-Nd1|957|CDS:1-957| 2\n", + "ENSMUST00000082396.1|ENSMUSG00000064345.1|-|-|mt-Nd2-201|mt-Nd2|1038|CDS:1-1038| 2\n", + "ENSMUST00000082402.1|ENSMUSG00000064351.1|-|-|mt-Co1-201|mt-Co1|1545|CDS:1-1545| 2\n", + "ENSMUST00000082405.1|ENSMUSG00000064354.1|-|-|mt-Co2-201|mt-Co2|684|CDS:1-684| 2\n", + "ENSMUST00000082407.1|ENSMUSG00000064356.3|-|-|mt-Atp8-201|mt-Atp8|204|CDS:1-204| 2\n", + "ENSMUST00000082408.1|ENSMUSG00000064357.1|-|-|mt-Atp6-201|mt-Atp6|681|CDS:1-681| 2\n", + "ENSMUST00000082409.1|ENSMUSG00000064358.1|-|-|mt-Co3-201|mt-Co3|784|CDS:1-784| 2\n", + "ENSMUST00000082411.1|ENSMUSG00000064360.1|-|-|mt-Nd3-201|mt-Nd3|348|CDS:1-348| 2\n", + "ENSMUST00000084013.1|ENSMUSG00000065947.3|-|-|mt-Nd4l-201|mt-Nd4l|297|CDS:1-297| 2\n", + "ENSMUST00000082414.1|ENSMUSG00000064363.1|-|-|mt-Nd4-201|mt-Nd4|1378|CDS:1-1378| 2\n", + "ENSMUST00000082418.1|ENSMUSG00000064367.1|-|-|mt-Nd5-201|mt-Nd5|1824|CDS:1-1824| 2\n", + "ENSMUST00000082419.1|ENSMUSG00000064368.1|-|-|mt-Nd6-201|mt-Nd6|519|CDS:1-519| 2\n", + "ENSMUST00000082421.1|ENSMUSG00000064370.1|-|-|mt-Cytb-201|mt-Cytb|1144|CDS:1-1144| 2\n", + "dtype: int64" + ] + }, + "execution_count": 53, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "(kallisto_log2_tpm > 1).sum(axis=1)" ] @@ -762,7 +2075,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 54, "metadata": { "collapsed": false, "deletable": false, @@ -774,7 +2087,80 @@ "solution": false } }, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "target_id\n", + "ENSMUST00000070533.4|ENSMUSG00000051951.5|OTTMUSG00000026353.2|OTTMUST00000065166.1|Xkr4-001|Xkr4|3634|UTR5:1-150|CDS:151-2094|UTR3:2095-3634| False\n", + "ENSMUST00000194992.5|ENSMUSG00000025900.10|OTTMUSG00000049985.2|OTTMUST00000127194.1|Rp1-002|Rp1|3047|UTR5:1-54|CDS:55-912|UTR3:913-3047| False\n", + "ENSMUST00000027032.5|ENSMUSG00000025900.10|OTTMUSG00000049985.2|OTTMUST00000127195.2|Rp1-001|Rp1|6869|UTR5:1-127|CDS:128-6415|UTR3:6416-6869| False\n", + "ENSMUST00000027035.9|ENSMUSG00000025902.13|OTTMUSG00000050014.7|OTTMUST00000127245.2|Sox17-001|Sox17|3127|UTR5:1-1082|CDS:1083-2342|UTR3:2343-3127| False\n", + "ENSMUST00000195555.1|ENSMUSG00000025902.13|OTTMUSG00000050014.7|OTTMUST00000127249.1|Sox17-005|Sox17|1977|UTR5:1-635|CDS:636-1511|UTR3:1512-1977| False\n", + "ENSMUST00000192650.5|ENSMUSG00000025902.13|OTTMUSG00000050014.7|OTTMUST00000127247.2|Sox17-004|Sox17|3242|UTR5:1-1851|CDS:1852-2916|UTR3:2917-3242| False\n", + "ENSMUST00000116652.7|ENSMUSG00000025902.13|OTTMUSG00000050014.7|OTTMUST00000127246.1|Sox17-002|Sox17|1512|UTR5:1-249|CDS:250-1509|UTR3:1510-1512| False\n", + "ENSMUST00000191647.1|ENSMUSG00000025902.13|OTTMUSG00000050014.7|OTTMUST00000127267.2|Sox17-007|Sox17|406|UTR5:1-83|CDS:84-406| False\n", + "ENSMUST00000191939.1|ENSMUSG00000025902.13|OTTMUSG00000050014.7|OTTMUST00000127266.2|Sox17-006|Sox17|840|UTR5:1-329|CDS:330-840| False\n", + "ENSMUST00000192913.1|ENSMUSG00000025902.13|OTTMUSG00000050014.7|OTTMUST00000127248.2|Sox17-003|Sox17|1506|UTR5:1-997|CDS:998-1506| False\n", + "ENSMUST00000130201.7|ENSMUSG00000033845.13|OTTMUSG00000029329.3|OTTMUST00000072660.1|Mrpl15-002|Mrpl15|1894|UTR5:1-33|CDS:34-648|UTR3:649-1894| False\n", + "ENSMUST00000156816.6|ENSMUSG00000033845.13|OTTMUSG00000029329.3|OTTMUST00000072659.1|Mrpl15-001|Mrpl15|4203|UTR5:1-62|CDS:63-950|UTR3:951-4203| False\n", + "ENSMUST00000045689.13|ENSMUSG00000033845.13|OTTMUSG00000029329.3|OTTMUST00000072661.1|Mrpl15-003|Mrpl15|497|UTR5:1-21|CDS:22-180|UTR3:181-497| False\n", + "ENSMUST00000146665.2|ENSMUSG00000033845.13|OTTMUSG00000029329.3|OTTMUST00000072662.2|Mrpl15-004|Mrpl15|1569|UTR5:1-62|CDS:63-569|UTR3:570-1569| True\n", + "ENSMUST00000134384.7|ENSMUSG00000025903.14|OTTMUSG00000021562.4|OTTMUST00000051163.2|Lypla1-002|Lypla1|1136|UTR5:1-126|CDS:127-801|UTR3:802-1136| True\n", + "ENSMUST00000027036.10|ENSMUSG00000025903.14|OTTMUSG00000021562.4|OTTMUST00000051162.1|Lypla1-001|Lypla1|2507|UTR5:1-91|CDS:92-784|UTR3:785-2507| True\n", + "ENSMUST00000150971.7|ENSMUSG00000025903.14|OTTMUSG00000021562.4|OTTMUST00000051164.3|Lypla1-003|Lypla1|877|UTR5:1-84|CDS:85-750|UTR3:751-877| False\n", + "ENSMUST00000119612.8|ENSMUSG00000025903.14|OTTMUSG00000021562.4|OTTMUST00000051170.2|Lypla1-009|Lypla1|529|UTR5:1-18|CDS:19-297|UTR3:298-529| False\n", + "ENSMUST00000137887.7|ENSMUSG00000025903.14|OTTMUSG00000021562.4|OTTMUST00000051168.2|Lypla1-007|Lypla1|444|UTR5:1-16|CDS:17-444| False\n", + "ENSMUST00000115529.7|ENSMUSG00000025903.14|OTTMUSG00000021562.4|OTTMUST00000051169.1|Lypla1-008|Lypla1|930|UTR5:1-3|CDS:4-594|UTR3:595-930| False\n", + "ENSMUST00000131119.1|ENSMUSG00000025903.14|OTTMUSG00000021562.4|OTTMUST00000051167.3|Lypla1-006|Lypla1|660|UTR5:1-234|CDS:235-660| False\n", + "ENSMUST00000155020.1|ENSMUSG00000104217.1|OTTMUSG00000050100.1|OTTMUST00000127419.1|Gm37988-001|Gm37988|825|UTR5:1-22|CDS:23-211|UTR3:212-825| False\n", + "ENSMUST00000081551.13|ENSMUSG00000033813.15|OTTMUSG00000042348.1|OTTMUST00000111602.1|Tcea1-001|Tcea1|2547|UTR5:1-100|CDS:101-1006|UTR3:1007-2547| True\n", + "ENSMUST00000165720.2|ENSMUSG00000033813.15|OTTMUSG00000042348.1|OTTMUST00000111603.1|Tcea1-002|Tcea1|2854|UTR5:1-370|CDS:371-1309|UTR3:1310-2854| False\n", + "ENSMUST00000002533.14|ENSMUSG00000002459.17|OTTMUSG00000029338.4|OTTMUST00000072687.1|Rgs20-002|Rgs20|1778|UTR5:1-160|CDS:161-880|UTR3:881-1778| True\n", + "ENSMUST00000118000.7|ENSMUSG00000002459.17|OTTMUSG00000029338.4|OTTMUST00000072688.2|Rgs20-001|Rgs20|2125|UTR5:1-108|CDS:109-1227|UTR3:1228-2125| False\n", + "ENSMUST00000119256.7|ENSMUSG00000002459.17|OTTMUSG00000029338.4|OTTMUST00000072706.2|Rgs20-005|Rgs20|883|UTR5:1-184|CDS:185-811|UTR3:812-883| False\n", + "ENSMUST00000170566.1|ENSMUSG00000002459.17|OTTMUSG00000029338.4|OTTMUST00000092053.1|Rgs20-007|Rgs20|577|CDS:1-120|UTR3:121-577| False\n", + "ENSMUST00000147158.1|ENSMUSG00000002459.17|OTTMUSG00000029338.4|OTTMUST00000072705.2|Rgs20-004|Rgs20|707|UTR5:1-105|CDS:106-707| False\n", + "ENSMUST00000192847.5|ENSMUSG00000033793.12|OTTMUSG00000050145.9|OTTMUST00000127492.1|Atp6v1h-003|Atp6v1h|1662|UTR5:1-161|CDS:162-1487|UTR3:1488-1662| True\n", + " ... \n", + "ENSMUST00000178889.1|ENSMUSG00000095650.2|OTTMUSG00000042966.1|-|Gm20854-201|Gm20854|1002|UTR5:1-175|CDS:176-859|UTR3:860-1002| False\n", + "ENSMUST00000181549.1|ENSMUSG00000095650.2|OTTMUSG00000042966.1|OTTMUST00000112802.1|Gm20854-001|Gm20854|1156|UTR5:1-335|CDS:336-1019|UTR3:1020-1156| False\n", + "ENSMUST00000188754.1|ENSMUSG00000100240.1|OTTMUSG00000047031.1|OTTMUST00000121805.1|Gm20820-001|Gm20820|921|UTR5:1-58|CDS:59-727|UTR3:728-921| False\n", + "ENSMUST00000189543.6|ENSMUSG00000094399.7|OTTMUSG00000047083.1|OTTMUST00000121876.1|Gm21477-001|Gm21477|924|UTR5:1-58|CDS:59-727|UTR3:728-924| False\n", + "ENSMUST00000179970.1|ENSMUSG00000094399.7|OTTMUSG00000047083.1|-|Gm21477-201|Gm21477|498|CDS:1-498| False\n", + "ENSMUST00000186493.1|ENSMUSG00000099856.1|OTTMUSG00000047138.1|OTTMUST00000121968.1|Gm20906-001|Gm20906|923|UTR5:1-58|CDS:59-727|UTR3:728-923| False\n", + "ENSMUST00000187146.1|ENSMUSG00000101915.1|OTTMUSG00000047149.1|OTTMUST00000121980.1|Gm28102-001|Gm28102|924|UTR5:1-58|CDS:59-727|UTR3:728-924| False\n", + "ENSMUST00000186443.1|ENSMUSG00000102045.1|OTTMUSG00000047309.1|OTTMUST00000122306.1|Gm21294-001|Gm21294|934|UTR5:1-73|CDS:74-742|UTR3:743-934| False\n", + "ENSMUST00000188269.1|ENSMUSG00000100608.1|OTTMUSG00000047316.1|OTTMUST00000122318.1|Gm21996-001|Gm21996|931|UTR5:1-58|CDS:59-727|UTR3:728-931| False\n", + "ENSMUST00000190558.6|ENSMUSG00000096178.7|OTTMUSG00000047352.1|OTTMUST00000122361.1|Gm20837-001|Gm20837|844|UTR5:1-73|CDS:74-640|UTR3:641-844| False\n", + "ENSMUST00000178446.1|ENSMUSG00000096178.7|OTTMUSG00000047352.1|-|Gm20837-201|Gm20837|498|CDS:1-498| False\n", + "ENSMUST00000177893.1|ENSMUSG00000095366.1|-|-|Gm21860-201|Gm21860|309|CDS:1-309| False\n", + "ENSMUST00000179483.7|ENSMUSG00000096768.7|-|-|Erdr1-204|Erdr1|688|UTR5:1-70|CDS:71-688| False\n", + "ENSMUST00000177591.1|ENSMUSG00000096768.7|-|-|Erdr1-201|Erdr1|774|UTR5:1-229|CDS:230-757|UTR3:758-774| False\n", + "ENSMUST00000177671.7|ENSMUSG00000096768.7|-|-|Erdr1-202|Erdr1|708|UTR5:1-159|CDS:160-528|UTR3:529-708| False\n", + "ENSMUST00000179077.1|ENSMUSG00000096768.7|-|-|Erdr1-203|Erdr1|887|UTR5:1-74|CDS:75-512|UTR3:513-887| False\n", + "ENSMUST00000179623.1|ENSMUSG00000096850.1|-|-|Gm21748-201|Gm21748|309|CDS:1-309| False\n", + "ENSMUST00000082392.1|ENSMUSG00000064341.1|-|-|mt-Nd1-201|mt-Nd1|957|CDS:1-957| True\n", + "ENSMUST00000082396.1|ENSMUSG00000064345.1|-|-|mt-Nd2-201|mt-Nd2|1038|CDS:1-1038| True\n", + "ENSMUST00000082402.1|ENSMUSG00000064351.1|-|-|mt-Co1-201|mt-Co1|1545|CDS:1-1545| True\n", + "ENSMUST00000082405.1|ENSMUSG00000064354.1|-|-|mt-Co2-201|mt-Co2|684|CDS:1-684| True\n", + "ENSMUST00000082407.1|ENSMUSG00000064356.3|-|-|mt-Atp8-201|mt-Atp8|204|CDS:1-204| True\n", + "ENSMUST00000082408.1|ENSMUSG00000064357.1|-|-|mt-Atp6-201|mt-Atp6|681|CDS:1-681| True\n", + "ENSMUST00000082409.1|ENSMUSG00000064358.1|-|-|mt-Co3-201|mt-Co3|784|CDS:1-784| True\n", + "ENSMUST00000082411.1|ENSMUSG00000064360.1|-|-|mt-Nd3-201|mt-Nd3|348|CDS:1-348| True\n", + "ENSMUST00000084013.1|ENSMUSG00000065947.3|-|-|mt-Nd4l-201|mt-Nd4l|297|CDS:1-297| True\n", + "ENSMUST00000082414.1|ENSMUSG00000064363.1|-|-|mt-Nd4-201|mt-Nd4|1378|CDS:1-1378| True\n", + "ENSMUST00000082418.1|ENSMUSG00000064367.1|-|-|mt-Nd5-201|mt-Nd5|1824|CDS:1-1824| True\n", + "ENSMUST00000082419.1|ENSMUSG00000064368.1|-|-|mt-Nd6-201|mt-Nd6|519|CDS:1-519| True\n", + "ENSMUST00000082421.1|ENSMUSG00000064370.1|-|-|mt-Cytb-201|mt-Cytb|1144|CDS:1-1144| True\n", + "dtype: bool" + ] + }, + "execution_count": 54, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "(kallisto_log2_tpm > 1).sum(axis=1) >= 1" ] @@ -797,7 +2183,7 @@ }, { "cell_type": "code", - "execution_count": null, + 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s10s13
target_id
ENSMUST00000146665.2|ENSMUSG00000033845.13|OTTMUSG00000029329.3|OTTMUST00000072662.2|Mrpl15-004|Mrpl15|1569|UTR5:1-62|CDS:63-569|UTR3:570-1569|0.0000003.952259
ENSMUST00000134384.7|ENSMUSG00000025903.14|OTTMUSG00000021562.4|OTTMUST00000051163.2|Lypla1-002|Lypla1|1136|UTR5:1-126|CDS:127-801|UTR3:802-1136|0.2786692.769812
ENSMUST00000027036.10|ENSMUSG00000025903.14|OTTMUSG00000021562.4|OTTMUST00000051162.1|Lypla1-001|Lypla1|2507|UTR5:1-91|CDS:92-784|UTR3:785-2507|3.1747842.992448
ENSMUST00000081551.13|ENSMUSG00000033813.15|OTTMUSG00000042348.1|OTTMUST00000111602.1|Tcea1-001|Tcea1|2547|UTR5:1-100|CDS:101-1006|UTR3:1007-2547|6.9473511.058026
ENSMUST00000002533.14|ENSMUSG00000002459.17|OTTMUSG00000029338.4|OTTMUST00000072687.1|Rgs20-002|Rgs20|1778|UTR5:1-160|CDS:161-880|UTR3:881-1778|2.7950654.141637
ENSMUST00000192847.5|ENSMUSG00000033793.12|OTTMUSG00000050145.9|OTTMUST00000127492.1|Atp6v1h-003|Atp6v1h|1662|UTR5:1-161|CDS:162-1487|UTR3:1488-1662|1.7744900.000000
ENSMUST00000159906.7|ENSMUSG00000025907.14|OTTMUSG00000033467.12|OTTMUST00000084214.2|Rb1cc1-009|Rb1cc1|656|UTR5:1-375|CDS:376-656|0.0000007.568701
ENSMUST00000088658.10|ENSMUSG00000025912.16|OTTMUSG00000034736.3|OTTMUST00000088260.1|Mybl1-001|Mybl1|4980|UTR5:1-255|CDS:256-2511|UTR3:2512-4980|0.7755181.389170
ENSMUST00000052843.11|ENSMUSG00000046101.16|OTTMUSG00000021854.3|OTTMUST00000051859.1|Mcmdc2-001|Mcmdc2|2826|UTR5:1-97|CDS:98-1141|UTR3:1142-2826|2.0367280.237117
ENSMUST00000118098.2|ENSMUSG00000046101.16|OTTMUSG00000021854.3|OTTMUST00000078010.2|Mcmdc2-003|Mcmdc2|2072|UTR5:1-405|CDS:406-1482|UTR3:1483-2072|0.2344142.070753
ENSMUST00000183059.1|ENSMUSG00000046101.16|OTTMUSG00000021854.3|OTTMUST00000113822.1|Mcmdc2-005|Mcmdc2|749|CDS:1-77|UTR3:78-749|7.0792718.468359
ENSMUST00000027050.9|ENSMUSG00000025917.9|OTTMUSG00000029459.3|OTTMUST00000072996.2|Cops5-001|Cops5|1698|UTR5:1-315|CDS:316-1320|UTR3:1321-1698|6.7233260.000000
ENSMUST00000186528.6|ENSMUSG00000025917.9|OTTMUSG00000029459.3|OTTMUST00000118982.1|Cops5-006|Cops5|962|UTR5:1-129|CDS:130-276|UTR3:277-962|4.8561290.246389
ENSMUST00000191012.6|ENSMUSG00000056763.16|OTTMUSG00000027401.8|OTTMUST00000118986.2|Cspp1-019|Cspp1|345|UTR5:1-135|CDS:136-345|4.3753310.000000
ENSMUST00000122156.7|ENSMUSG00000056763.16|OTTMUSG00000027401.8|OTTMUST00000067947.1|Cspp1-006|Cspp1|2535|UTR5:1-117|CDS:118-1077|UTR3:1078-2535|3.4666140.000000
ENSMUST00000155974.7|ENSMUSG00000056763.16|OTTMUSG00000027401.8|OTTMUST00000067949.4|Cspp1-008|Cspp1|445|UTR5:1-139|CDS:140-445|3.0358260.000000
ENSMUST00000188449.6|ENSMUSG00000056763.16|OTTMUSG00000027401.8|OTTMUST00000118993.1|Cspp1-024|Cspp1|538|CDS:1-317|UTR3:318-538|6.6190770.000000
ENSMUST00000088615.10|ENSMUSG00000067851.11|OTTMUSG00000033923.2|OTTMUST00000085577.1|Arfgef1-002|Arfgef1|6978|UTR5:1-176|CDS:177-5717|UTR3:5718-6978|6.2235232.219540
ENSMUST00000027056.11|ENSMUSG00000048960.13|OTTMUSG00000047927.1|OTTMUST00000123246.1|Prex2-001|Prex2|11053|UTR5:1-328|CDS:329-5125|UTR3:5126-11053|1.7368470.056283
ENSMUST00000188154.1|ENSMUSG00000048960.13|OTTMUSG00000047927.1|OTTMUST00000123253.1|Prex2-006|Prex2|843|CDS:1-122|UTR3:123-843|1.5475195.895499
ENSMUST00000171690.8|ENSMUSG00000057715.13|OTTMUSG00000033915.2|-|A830018L16Rik-201|A830018L16Rik|6158|UTR5:1-464|CDS:465-1331|UTR3:1332-6158|1.5973932.705801
ENSMUST00000188454.6|ENSMUSG00000025938.16|OTTMUSG00000022327.2|OTTMUST00000053228.2|Slco5a1-001|Slco5a1|8463|UTR5:1-591|CDS:592-3144|UTR3:3145-8463|0.0562843.506221
ENSMUST00000136197.7|ENSMUSG00000025938.16|OTTMUSG00000022327.2|OTTMUST00000053230.2|Slco5a1-003|Slco5a1|5123|UTR5:1-640|CDS:641-2617|UTR3:2618-5123|0.0271346.674800
ENSMUST00000027068.10|ENSMUSG00000025935.10|OTTMUSG00000049113.1|OTTMUST00000125384.1|Tram1-001|Tram1|2938|UTR5:1-188|CDS:189-1313|UTR3:1314-2938|5.4310710.201256
ENSMUST00000027071.6|ENSMUSG00000025937.6|OTTMUSG00000021599.3|OTTMUST00000051280.2|Lactb2-001|Lactb2|4494|UTR5:1-96|CDS:97-963|UTR3:964-4494|3.9405994.778224
ENSMUST00000041447.4|ENSMUSG00000032769.4|OTTMUSG00000049207.1|OTTMUST00000125545.1|Trpa1-001|Trpa1|4263|UTR5:1-27|CDS:28-3405|UTR3:3406-4263|0.0000002.086301
ENSMUST00000188371.6|ENSMUSG00000025925.14|OTTMUSG00000047984.2|OTTMUST00000123359.2|Terf1-001|Terf1|2268|UTR5:1-32|CDS:33-1298|UTR3:1299-2268|0.5358475.333087
ENSMUST00000115367.7|ENSMUSG00000067795.13|OTTMUSG00000022165.2|OTTMUST00000052635.1|4930444P10Rik-003|4930444P10Rik|868|UTR5:1-163|CDS:164-721|UTR3:722-868|3.5914044.592032
ENSMUST00000058437.13|ENSMUSG00000043716.13|OTTMUSG00000016936.3|OTTMUST00000041073.2|Rpl7-001|Rpl7|1163|UTR5:1-284|CDS:285-1097|UTR3:1098-1163|9.5577499.656554
ENSMUST00000149566.1|ENSMUSG00000043716.13|OTTMUSG00000016936.3|OTTMUST00000041075.2|Rpl7-003|Rpl7|838|CDS:1-838|8.0276357.302383
.........
ENSMUST00000112172.3|ENSMUSG00000049775.16|OTTMUSG00000019572.3|OTTMUST00000046738.1|Tmsb4x-001|Tmsb4x|768|UTR5:1-225|CDS:226-360|UTR3:361-768|13.76828814.830347
ENSMUST00000112176.7|ENSMUSG00000049775.16|OTTMUSG00000019572.3|OTTMUST00000046739.2|Tmsb4x-002|Tmsb4x|698|UTR5:1-139|CDS:140-292|UTR3:293-698|4.3587346.675759
ENSMUST00000112175.1|ENSMUSG00000049775.16|OTTMUSG00000019572.3|OTTMUST00000046740.1|Tmsb4x-003|Tmsb4x|864|UTR5:1-502|CDS:503-655|UTR3:656-864|0.6531298.543295
ENSMUST00000112137.1|ENSMUSG00000031358.17|OTTMUSG00000019558.2|OTTMUST00000046702.2|Msl3-002|Msl3|2316|UTR5:1-163|CDS:164-1564|UTR3:1565-2316|0.0943841.071969
ENSMUST00000112129.7|ENSMUSG00000031355.16|OTTMUSG00000019560.4|OTTMUST00000046950.1|Arhgap6-006|Arhgap6|2487|UTR5:1-211|CDS:212-1369|UTR3:1370-2487|2.2175632.394953
ENSMUST00000154638.8|ENSMUSG00000031352.10|OTTMUSG00000019596.2|OTTMUST00000046816.2|Hccs-003|Hccs|3310|UTR5:1-239|CDS:240-521|UTR3:522-3310|0.6934461.291150
ENSMUST00000033717.8|ENSMUSG00000031352.10|OTTMUSG00000019596.2|OTTMUST00000046815.1|Hccs-002|Hccs|2320|UTR5:1-207|CDS:208-1026|UTR3:1027-2320|5.2850360.090573
ENSMUST00000115894.2|ENSMUSG00000069053.11|OTTMUSG00000045273.1|-|Uba1y-201|Uba1y|3981|UTR5:1-102|CDS:103-3279|UTR3:3280-3981|2.2656623.909082
ENSMUST00000189069.6|ENSMUSG00000056673.14|OTTMUSG00000045277.1|OTTMUST00000118912.1|Kdm5d-004|Kdm5d|2177|UTR5:1-178|CDS:179-1609|UTR3:1610-2177|0.0000001.415645
ENSMUST00000055032.13|ENSMUSG00000056673.14|OTTMUSG00000045277.1|OTTMUST00000118913.1|Kdm5d-001|Kdm5d|7974|UTR5:1-176|CDS:177-4823|UTR3:4824-7974|3.0096523.433922
ENSMUST00000186726.6|ENSMUSG00000056673.14|OTTMUSG00000045277.1|OTTMUST00000118916.1|Kdm5d-002|Kdm5d|5916|UTR5:1-128|CDS:129-944|UTR3:945-5916|1.7155682.865436
ENSMUST00000143958.7|ENSMUSG00000068457.14|OTTMUSG00000032814.5|OTTMUST00000081730.2|Uty-002|Uty|2903|UTR5:1-126|CDS:127-363|UTR3:364-2903|1.1691300.000000
ENSMUST00000091190.11|ENSMUSG00000069045.11|OTTMUSG00000045279.1|OTTMUST00000118924.1|Ddx3y-001|Ddx3y|4600|UTR5:1-106|CDS:107-2083|UTR3:2084-4600|0.4201811.121188
ENSMUST00000091178.1|ENSMUSG00000069036.3|OTTMUSG00000045384.2|OTTMUST00000119113.2|Sry-001|Sry|1188|CDS:1-1188|2.3055091.958223
ENSMUST00000190391.1|ENSMUSG00000096706.2|OTTMUSG00000045647.2|OTTMUST00000119534.2|Gm21854-001|Gm21854|1480|UTR5:1-662|CDS:663-1361|UTR3:1362-1480|1.3864470.904086
ENSMUST00000185926.1|ENSMUSG00000096036.2|OTTMUSG00000045661.2|OTTMUST00000119556.2|Gm21778-001|Gm21778|1482|UTR5:1-660|CDS:661-1359|UTR3:1360-1482|3.4110560.000000
ENSMUST00000189201.1|ENSMUSG00000094484.2|OTTMUSG00000045867.2|OTTMUST00000119866.2|Gm21244-001|Gm21244|3115|UTR5:1-405|CDS:406-1089|UTR3:1090-3115|6.1084437.190151
ENSMUST00000082392.1|ENSMUSG00000064341.1|-|-|mt-Nd1-201|mt-Nd1|957|CDS:1-957|10.38611012.218548
ENSMUST00000082396.1|ENSMUSG00000064345.1|-|-|mt-Nd2-201|mt-Nd2|1038|CDS:1-1038|9.12867211.083306
ENSMUST00000082402.1|ENSMUSG00000064351.1|-|-|mt-Co1-201|mt-Co1|1545|CDS:1-1545|14.11068713.061822
ENSMUST00000082405.1|ENSMUSG00000064354.1|-|-|mt-Co2-201|mt-Co2|684|CDS:1-684|13.67325413.407600
ENSMUST00000082407.1|ENSMUSG00000064356.3|-|-|mt-Atp8-201|mt-Atp8|204|CDS:1-204|13.96062614.381415
ENSMUST00000082408.1|ENSMUSG00000064357.1|-|-|mt-Atp6-201|mt-Atp6|681|CDS:1-681|13.43556613.835251
ENSMUST00000082409.1|ENSMUSG00000064358.1|-|-|mt-Co3-201|mt-Co3|784|CDS:1-784|13.36691013.871424
ENSMUST00000082411.1|ENSMUSG00000064360.1|-|-|mt-Nd3-201|mt-Nd3|348|CDS:1-348|10.29168910.614544
ENSMUST00000084013.1|ENSMUSG00000065947.3|-|-|mt-Nd4l-201|mt-Nd4l|297|CDS:1-297|10.23593011.969117
ENSMUST00000082414.1|ENSMUSG00000064363.1|-|-|mt-Nd4-201|mt-Nd4|1378|CDS:1-1378|10.38015811.326160
ENSMUST00000082418.1|ENSMUSG00000064367.1|-|-|mt-Nd5-201|mt-Nd5|1824|CDS:1-1824|9.93843610.430975
ENSMUST00000082419.1|ENSMUSG00000064368.1|-|-|mt-Nd6-201|mt-Nd6|519|CDS:1-519|9.17278310.414791
ENSMUST00000082421.1|ENSMUSG00000064370.1|-|-|mt-Cytb-201|mt-Cytb|1144|CDS:1-1144|12.19256412.669727
\n", + "

9383 rows × 2 columns

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"execution_count": null, + "execution_count": 56, "metadata": { "collapsed": false, "deletable": false, @@ -846,7 +2633,76 @@ "solution": false } }, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "(9383, 2)\n" + ] + }, + { + "data": { + "text/html": [ + "
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s10s13
target_id
ENSMUST00000146665.2|ENSMUSG00000033845.13|OTTMUSG00000029329.3|OTTMUST00000072662.2|Mrpl15-004|Mrpl15|1569|UTR5:1-62|CDS:63-569|UTR3:570-1569|0.0000003.952259
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ENSMUST00000081551.13|ENSMUSG00000033813.15|OTTMUSG00000042348.1|OTTMUST00000111602.1|Tcea1-001|Tcea1|2547|UTR5:1-100|CDS:101-1006|UTR3:1007-2547|6.9473511.058026
ENSMUST00000002533.14|ENSMUSG00000002459.17|OTTMUSG00000029338.4|OTTMUST00000072687.1|Rgs20-002|Rgs20|1778|UTR5:1-160|CDS:161-880|UTR3:881-1778|2.7950654.141637
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" + ], + "text/plain": [ + " s10 s13\n", + "target_id \n", + "ENSMUST00000146665.2|ENSMUSG00000033845.13|OTTM... 0.000000 3.952259\n", + "ENSMUST00000134384.7|ENSMUSG00000025903.14|OTTM... 0.278669 2.769812\n", + "ENSMUST00000027036.10|ENSMUSG00000025903.14|OTT... 3.174784 2.992448\n", + "ENSMUST00000081551.13|ENSMUSG00000033813.15|OTT... 6.947351 1.058026\n", + "ENSMUST00000002533.14|ENSMUSG00000002459.17|OTT... 2.795065 4.141637" + ] + }, + "execution_count": 56, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "kallisto_log2_tpm_expressed = kallisto_log2_tpm.loc[expressed_genes]\n", "print(kallisto_log2_tpm_expressed.shape)\n", @@ -871,7 +2727,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 57, "metadata": { "collapsed": false, "deletable": false, @@ -883,7 +2739,36 @@ "solution": false } }, - "outputs": [], + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/home/ucsd-train12/anaconda3/lib/python3.5/site-packages/matplotlib/__init__.py:892: UserWarning: axes.color_cycle is deprecated and replaced with axes.prop_cycle; please use the latter.\n", + " warnings.warn(self.msg_depr % (key, alt_key))\n" + ] + }, + { + "data": { + "text/plain": [ + "" + ] + }, + "execution_count": 57, + "metadata": {}, + "output_type": "execute_result" + }, + { + "data": { + "image/png": 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VjeoZE/Xaj/p2tuuMcpH6mu/0jeKdvvhlAFfMbkvbWn1fys62maY4a+nDCFU3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\nqkQhAYC8iwk2bOnW3LUWAGRV18FirKn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QIiIiw2AoERGRYTCUiIjIMBhKRERkGAwlIiIy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\nTkSuQmCC\n", + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], "source": [ "sns.jointplot('s10', 's13', kallisto_log2_tpm_expressed)" ] @@ -906,7 +2791,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 58, "metadata": { "collapsed": false, "deletable": false, @@ -918,14 +2803,44 @@ "solution": true } }, - "outputs": [], + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/home/ucsd-train12/anaconda3/lib/python3.5/site-packages/matplotlib/__init__.py:892: UserWarning: axes.color_cycle is deprecated and replaced with axes.prop_cycle; please use the latter.\n", + " warnings.warn(self.msg_depr % (key, alt_key))\n" + ] + }, + { + "data": { + "text/plain": [ + "" + ] + }, + "execution_count": 58, + "metadata": {}, + "output_type": "execute_result" + }, + { + "data": { + "image/png": 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/7hmu+BMoC7GShVu1VbhWWXdnb3y+6GjvEFqaa5PLAoUjUcXCqqkVeKmhFo5E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\njDCXIMg0BJft8bcsma3YXDAUiSW3XFd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+ "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], "source": [ - "# YOUR CODE HERE" + "# YOUR CODE HERE\n", + "sns.jointplot('s10', 's13', kallisto_log2_tpm_expressed, stat_func=spearmanr)" ] }, { "cell_type": "code", - "execution_count": null, + "execution_count": 59, "metadata": { "collapsed": false, "deletable": false, @@ -961,7 +2876,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 60, "metadata": { "collapsed": false, "deletable": false, @@ -973,7 +2888,94 @@ "solution": false } }, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "(46984, 1)\n" + ] + }, + { + "data": { + "text/html": [ + "
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# Program:featureCounts v1.5.0; Command:\"featureCounts\" \"-T\" \"8\" \"-s\" \"-B\" \"--primary\" \"-a\" \"/projects/ps-yeolab/biom262-2016/genomes/mm10/gencode/m8/gencode.vM8.basic.annotation.gtf\" \"-o\" \"/home/ucsd-train12/projects/shalek2013/processed_data/s10_featureCounts.txt\" \"/home/ucsd-train12/projects/shalek2013/processed_data/S10.Aligned.out.sorted.bam\"
GeneidChrStartEndStrandLength/home/ucsd-train12/projects/shalek2013/process...
ENSMUSG00000102693.1chr130732533074322+10700
ENSMUSG00000064842.1chr131020163102125+110980
ENSMUSG00000051951.5chr1;chr1;chr13214482;3421702;36705523216968;3421901;3671498-;-;-36340
ENSMUSG00000102851.1chr132527573253236+4800
\n", + "
" + ], + "text/plain": [ + " # Program:featureCounts v1.5.0; Command:\"featureCounts\" \"-T\" \"8\" \"-s\" \"-B\" \"--primary\" \"-a\" \"/projects/ps-yeolab/biom262-2016/genomes/mm10/gencode/m8/gencode.vM8.basic.annotation.gtf\" \"-o\" \"/home/ucsd-train12/projects/shalek2013/processed_data/s10_featureCounts.txt\" \"/home/ucsd-train12/projects/shalek2013/processed_data/S10.Aligned.out.sorted.bam\" \n", + "Geneid Chr Start End Strand Length /home/ucsd-train12/projects/shalek2013/process... \n", + "ENSMUSG00000102693.1 chr1 3073253 3074322 + 1070 0 \n", + "ENSMUSG00000064842.1 chr1 3102016 3102125 + 110 980 \n", + "ENSMUSG00000051951.5 chr1;chr1;chr1 3214482;3421702;3670552 3216968;3421901;3671498 -;-;- 3634 0 \n", + "ENSMUSG00000102851.1 chr1 3252757 3253236 + 480 0 " + ] + }, + "execution_count": 60, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "s10_featurecounts = pd.read_table('s10_featureCounts.txt')\n", "print(s10_featurecounts.shape)\n", @@ -1001,7 +3003,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 61, "metadata": { "collapsed": false, "deletable": false, @@ -1013,16 +3015,130 @@ "solution": true } }, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "(46983, 6)\n" + ] + }, + { + "data": { + "text/html": [ + "
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ChrStartEndStrandLength/home/ucsd-train12/projects/shalek2013/processed_data/S10.Aligned.out.sorted.bam
Geneid
ENSMUSG00000102693.1chr130732533074322+10700
ENSMUSG00000064842.1chr131020163102125+110980
ENSMUSG00000051951.5chr1;chr1;chr13214482;3421702;36705523216968;3421901;3671498-;-;-36340
ENSMUSG00000102851.1chr132527573253236+4800
ENSMUSG00000103377.1chr133657313368549-28190
\n", + "
" + ], + "text/plain": [ + " Chr Start \\\n", + "Geneid \n", + "ENSMUSG00000102693.1 chr1 3073253 \n", + "ENSMUSG00000064842.1 chr1 3102016 \n", + "ENSMUSG00000051951.5 chr1;chr1;chr1 3214482;3421702;3670552 \n", + "ENSMUSG00000102851.1 chr1 3252757 \n", + "ENSMUSG00000103377.1 chr1 3365731 \n", + "\n", + " End Strand Length \\\n", + "Geneid \n", + "ENSMUSG00000102693.1 3074322 + 1070 \n", + "ENSMUSG00000064842.1 3102125 + 110 \n", + "ENSMUSG00000051951.5 3216968;3421901;3671498 -;-;- 3634 \n", + "ENSMUSG00000102851.1 3253236 + 480 \n", + "ENSMUSG00000103377.1 3368549 - 2819 \n", + "\n", + " /home/ucsd-train12/projects/shalek2013/processed_data/S10.Aligned.out.sorted.bam \n", + "Geneid \n", + "ENSMUSG00000102693.1 0 \n", + "ENSMUSG00000064842.1 980 \n", + "ENSMUSG00000051951.5 0 \n", + "ENSMUSG00000102851.1 0 \n", + "ENSMUSG00000103377.1 0 " + ] + }, + "execution_count": 61, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "# YOUR CODE HERE\n", + "s10_featurecounts = pd.read_table('s10_featureCounts.txt', skiprows=1, index_col=0)\n", "print(s10_featurecounts.shape)\n", "s10_featurecounts.head()" ] }, { "cell_type": "code", - "execution_count": null, + "execution_count": 6, "metadata": { "collapsed": false, "deletable": false, @@ -1065,7 +3181,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 7, "metadata": { "collapsed": false, "deletable": false, @@ -1077,7 +3193,24 @@ "solution": false } }, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "Chr object\n", + "Start object\n", + "End object\n", + "Strand object\n", + "Length int64\n", + "/home/ucsd-train12/projects/shalek2013/processed_data/S10.Aligned.out.sorted.bam int64\n", + "dtype: object" + ] + }, + "execution_count": 7, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "s10_featurecounts.dtypes" ] @@ -1100,7 +3233,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 8, "metadata": { "collapsed": false, "deletable": false, @@ -1113,9 +3246,30 @@ }, "scrolled": true }, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "" + ] + }, + "execution_count": 8, + "metadata": {}, + "output_type": "execute_result" + }, + { + "data": { + "image/png": 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+ "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], "source": [ - "sns.distplot(s10_featurecounts['/home/ucsd-train01/projects/shalek2013/processed_data/S10.Aligned.out.sorted.bam'])" + "sns.distplot(s10_featurecounts['/home/ucsd-train12/projects/shalek2013/processed_data/S10.Aligned.out.sorted.bam'])" ] }, { @@ -1136,7 +3290,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 9, "metadata": { "collapsed": false, "deletable": false, @@ -1148,7 +3302,18 @@ "solution": false } }, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "90730267" + ] + }, + "execution_count": 9, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "s10_featurecounts['Length'].sum()" ] @@ -1173,7 +3338,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 10, "metadata": { "collapsed": false, "deletable": false, @@ -1183,16 +3348,160 @@ "grade_id": "show_make_other_columns", "locked": true, "solution": false - } + }, + "scrolled": true }, - "outputs": [], - "source": [ - "reads = s10_featurecounts['/home/ucsd-train01/projects/shalek2013/processed_data/S10.Aligned.out.sorted.bam']\n", - "\n", + "outputs": [ + { + "data": { + "text/html": [ + "
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ChrStartEndStrandLength/home/ucsd-train12/projects/shalek2013/processed_data/S10.Aligned.out.sorted.bamnew_column
Geneid
ENSMUSG00000102693.1chr130732533074322+107000.00
ENSMUSG00000064842.1chr131020163102125+11098044457830.83
ENSMUSG00000051951.5chr1;chr1;chr13214482;3421702;36705523216968;3421901;3671498-;-;-363400.00
ENSMUSG00000102851.1chr132527573253236+48000.00
ENSMUSG00000103377.1chr133657313368549-281900.00
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ChrStartEndStrandLength/home/ucsd-train12/projects/shalek2013/processed_data/S10.Aligned.out.sorted.bamfpkm
Geneid
ENSMUSG00000102693.1chr130732533074322+107000.000000
ENSMUSG00000064842.1chr131020163102125+110980191.794717
ENSMUSG00000051951.5chr1;chr1;chr13214482;3421702;36705523216968;3421901;3671498-;-;-363400.000000
ENSMUSG00000102851.1chr132527573253236+48000.000000
ENSMUSG00000103377.1chr133657313368549-281900.000000
\n", + "
" + ], + "text/plain": [ + " Chr Start \\\n", + "Geneid \n", + "ENSMUSG00000102693.1 chr1 3073253 \n", + "ENSMUSG00000064842.1 chr1 3102016 \n", + "ENSMUSG00000051951.5 chr1;chr1;chr1 3214482;3421702;3670552 \n", + "ENSMUSG00000102851.1 chr1 3252757 \n", + "ENSMUSG00000103377.1 chr1 3365731 \n", + "\n", + " End Strand Length \\\n", + "Geneid \n", + "ENSMUSG00000102693.1 3074322 + 1070 \n", + "ENSMUSG00000064842.1 3102125 + 110 \n", + "ENSMUSG00000051951.5 3216968;3421901;3671498 -;-;- 3634 \n", + "ENSMUSG00000102851.1 3253236 + 480 \n", + "ENSMUSG00000103377.1 3368549 - 2819 \n", + "\n", + " /home/ucsd-train12/projects/shalek2013/processed_data/S10.Aligned.out.sorted.bam \\\n", + "Geneid \n", + "ENSMUSG00000102693.1 0 \n", + "ENSMUSG00000064842.1 980 \n", + "ENSMUSG00000051951.5 0 \n", + "ENSMUSG00000102851.1 0 \n", + "ENSMUSG00000103377.1 0 \n", + "\n", + " fpkm \n", + "Geneid \n", + "ENSMUSG00000102693.1 0.000000 \n", + "ENSMUSG00000064842.1 191.794717 \n", + "ENSMUSG00000051951.5 0.000000 \n", + "ENSMUSG00000102851.1 0.000000 \n", + "ENSMUSG00000103377.1 0.000000 " + ] + }, + "execution_count": 66, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "reads = s10_featurecounts['/home/ucsd-train12/projects/shalek2013/processed_data/S10.Aligned.out.sorted.bam']\n", + "s10_featurecounts['fpkm'] = (reads * 1e9)/(reads.sum() * s10_featurecounts.Length)\n", "s10_featurecounts.head()" ] }, { "cell_type": "code", - "execution_count": null, + "execution_count": 17, + "metadata": { + "collapsed": false + }, + "outputs": [ + { + "data": { + "text/plain": [ + "46451180" + ] + }, + "execution_count": 17, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "reads.sum()" + ] + }, + { + "cell_type": "code", + "execution_count": 67, "metadata": { "collapsed": false, "deletable": false, @@ -1249,9 +3699,22 @@ "locked": true, "points": 5, "solution": false - } + }, + "scrolled": true }, - "outputs": [], + "outputs": [ + { + "ename": "AssertionError", + "evalue": "", + "output_type": "error", + "traceback": [ + "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[1;31mAssertionError\u001b[0m Traceback (most recent call last)", + "\u001b[1;32m\u001b[0m in \u001b[0;36m\u001b[1;34m()\u001b[0m\n\u001b[1;32m----> 1\u001b[1;33m \u001b[1;32massert\u001b[0m \u001b[0ms10_featurecounts\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mloc\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;34m'ENSMUSG00000064842.1'\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;34m'fpkm'\u001b[0m\u001b[1;33m]\u001b[0m \u001b[1;33m==\u001b[0m \u001b[1;36m151.9538381109796\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m", + "\u001b[1;31mAssertionError\u001b[0m: " + ] + } + ], "source": [ "assert s10_featurecounts.loc['ENSMUSG00000064842.1', 'fpkm'] == 151.9538381109796" ] @@ -1274,7 +3737,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 68, "metadata": { "collapsed": false, "deletable": false, @@ -1284,13 +3747,57 @@ "grade_id": "show_fpkm_distribution", "locked": true, "solution": false - } + }, + "scrolled": true }, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "" + ] + }, + "execution_count": 68, + "metadata": {}, + "output_type": "execute_result" + }, + { + "data": { + "image/png": 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+ "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], "source": [ "sns.distplot(s10_featurecounts['fpkm'])" ] }, + { + "cell_type": "code", + "execution_count": 69, + "metadata": { + "collapsed": false + }, + "outputs": [ + { + "data": { + "text/plain": [ + "90730267" + ] + }, + "execution_count": 69, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "s10_featurecounts['Length'].sum()" + ] + }, { "cell_type": "markdown", "metadata": { @@ -1313,7 +3820,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 70, "metadata": { "collapsed": false, "deletable": false, @@ -1325,15 +3832,144 @@ "solution": true } }, - "outputs": [], + "outputs": [ + { + "data": { + "text/html": [ + "
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ChrStartEndStrandLength/home/ucsd-train12/projects/shalek2013/processed_data/S10.Aligned.out.sorted.bamfpkmtpm
Geneid
ENSMUSG00000102693.1chr130732533074322+107000.0000000.000000
ENSMUSG00000064842.1chr131020163102125+110980191.794717320.193945
ENSMUSG00000051951.5chr1;chr1;chr13214482;3421702;36705523216968;3421901;3671498-;-;-363400.0000000.000000
ENSMUSG00000102851.1chr132527573253236+48000.0000000.000000
ENSMUSG00000103377.1chr133657313368549-281900.0000000.000000
\n", + "
" + ], + "text/plain": [ + " Chr Start \\\n", + "Geneid \n", + "ENSMUSG00000102693.1 chr1 3073253 \n", + "ENSMUSG00000064842.1 chr1 3102016 \n", + "ENSMUSG00000051951.5 chr1;chr1;chr1 3214482;3421702;3670552 \n", + "ENSMUSG00000102851.1 chr1 3252757 \n", + "ENSMUSG00000103377.1 chr1 3365731 \n", + "\n", + " End Strand Length \\\n", + "Geneid \n", + "ENSMUSG00000102693.1 3074322 + 1070 \n", + "ENSMUSG00000064842.1 3102125 + 110 \n", + "ENSMUSG00000051951.5 3216968;3421901;3671498 -;-;- 3634 \n", + "ENSMUSG00000102851.1 3253236 + 480 \n", + "ENSMUSG00000103377.1 3368549 - 2819 \n", + "\n", + " /home/ucsd-train12/projects/shalek2013/processed_data/S10.Aligned.out.sorted.bam \\\n", + "Geneid \n", + "ENSMUSG00000102693.1 0 \n", + "ENSMUSG00000064842.1 980 \n", + "ENSMUSG00000051951.5 0 \n", + "ENSMUSG00000102851.1 0 \n", + "ENSMUSG00000103377.1 0 \n", + "\n", + " fpkm tpm \n", + "Geneid \n", + "ENSMUSG00000102693.1 0.000000 0.000000 \n", + "ENSMUSG00000064842.1 191.794717 320.193945 \n", + "ENSMUSG00000051951.5 0.000000 0.000000 \n", + "ENSMUSG00000102851.1 0.000000 0.000000 \n", + "ENSMUSG00000103377.1 0.000000 0.000000 " + ] + }, + "execution_count": 70, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "# YOUR CODE HERE\n", + "s10_featurecounts['tpm'] = (s10_featurecounts.fpkm * 1e6)/s10_featurecounts['fpkm'].sum()\n", "s10_featurecounts.head()" ] }, { "cell_type": "code", - "execution_count": null, + "execution_count": 71, "metadata": { "collapsed": false, "deletable": false, @@ -1346,7 +3982,19 @@ "solution": false } }, - "outputs": [], + "outputs": [ + { + "ename": "AssertionError", + "evalue": "", + "output_type": "error", + "traceback": [ + "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[1;31mAssertionError\u001b[0m Traceback (most recent call last)", + "\u001b[1;32m\u001b[0m in \u001b[0;36m\u001b[1;34m()\u001b[0m\n\u001b[1;32m----> 1\u001b[1;33m \u001b[1;32massert\u001b[0m \u001b[0ms10_featurecounts\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mloc\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;34m'ENSMUSG00000064842.1'\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;34m'tpm'\u001b[0m\u001b[1;33m]\u001b[0m \u001b[1;33m==\u001b[0m \u001b[1;36m260.82736102245372\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m", + "\u001b[1;31mAssertionError\u001b[0m: " + ] + } + ], "source": [ "assert s10_featurecounts.loc['ENSMUSG00000064842.1', 'tpm'] == 260.82736102245372" ] @@ -1369,7 +4017,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 72, "metadata": { "collapsed": false, "deletable": false, @@ -1381,7 +4029,28 @@ "solution": false } }, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "" + ] + }, + "execution_count": 72, + "metadata": {}, + "output_type": "execute_result" + }, + { + "data": { + "image/png": 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+ "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], "source": [ "sns.distplot(s10_featurecounts['tpm'])" ] @@ -1404,7 +4073,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 31, "metadata": { "collapsed": false, "deletable": false, @@ -1416,7 +4085,36 @@ "solution": false } }, - "outputs": [], + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/home/ucsd-train12/anaconda3/lib/python3.5/site-packages/matplotlib/__init__.py:892: UserWarning: axes.color_cycle is deprecated and replaced with axes.prop_cycle; please use the latter.\n", + " warnings.warn(self.msg_depr % (key, alt_key))\n" + ] + }, + { + "data": { + "text/plain": [ + "" + ] + }, + "execution_count": 31, + "metadata": {}, + "output_type": "execute_result" + }, + { + "data": { + "image/png": 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ENSMUSG00000103377.1chr133657313368549-281900.0000000.0000000.000000
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" + ], + "text/plain": [ + " Chr Start \\\n", + "Geneid \n", + "ENSMUSG00000102693.1 chr1 3073253 \n", + "ENSMUSG00000064842.1 chr1 3102016 \n", + "ENSMUSG00000051951.5 chr1;chr1;chr1 3214482;3421702;3670552 \n", + "ENSMUSG00000102851.1 chr1 3252757 \n", + "ENSMUSG00000103377.1 chr1 3365731 \n", + "\n", + " End Strand Length \\\n", + "Geneid \n", + "ENSMUSG00000102693.1 3074322 + 1070 \n", + "ENSMUSG00000064842.1 3102125 + 110 \n", + "ENSMUSG00000051951.5 3216968;3421901;3671498 -;-;- 3634 \n", + "ENSMUSG00000102851.1 3253236 + 480 \n", + "ENSMUSG00000103377.1 3368549 - 2819 \n", + "\n", + " /home/ucsd-train12/projects/shalek2013/processed_data/S10.Aligned.out.sorted.bam \\\n", + "Geneid \n", + "ENSMUSG00000102693.1 0 \n", + "ENSMUSG00000064842.1 980 \n", + "ENSMUSG00000051951.5 0 \n", + "ENSMUSG00000102851.1 0 \n", + "ENSMUSG00000103377.1 0 \n", + "\n", + " fpkm tpm log2_tpm \n", + "Geneid \n", + "ENSMUSG00000102693.1 0.000000 0.000000 0.000000 \n", + "ENSMUSG00000064842.1 191.794717 320.193945 8.327301 \n", + "ENSMUSG00000051951.5 0.000000 0.000000 0.000000 \n", + "ENSMUSG00000102851.1 0.000000 0.000000 0.000000 \n", + "ENSMUSG00000103377.1 0.000000 0.000000 0.000000 " + ] + }, + "execution_count": 80, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "# YOUR CODE HERE\n", + "s10_featurecounts['log2_tpm'] = np.log2(s10_featurecounts['tpm']+1)\n", "s10_featurecounts.head()" ] }, { "cell_type": "code", - "execution_count": null, + "execution_count": 81, "metadata": { "collapsed": false, "deletable": false, @@ -1474,7 +4308,19 @@ "solution": false } }, - "outputs": [], + "outputs": [ + { + "ename": "AssertionError", + "evalue": "", + "output_type": "error", + "traceback": [ + "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[1;31mAssertionError\u001b[0m Traceback (most recent call last)", + "\u001b[1;32m\u001b[0m in \u001b[0;36m\u001b[1;34m()\u001b[0m\n\u001b[1;32m----> 1\u001b[1;33m \u001b[1;32massert\u001b[0m \u001b[0ms10_featurecounts\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mloc\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;34m'ENSMUSG00000064842.1'\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;34m'log2_tpm'\u001b[0m\u001b[1;33m]\u001b[0m \u001b[1;33m==\u001b[0m \u001b[1;36m8.0324720569159176\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m", + "\u001b[1;31mAssertionError\u001b[0m: " + ] + } + ], "source": [ "assert s10_featurecounts.loc['ENSMUSG00000064842.1', 'log2_tpm'] == 8.0324720569159176" ] @@ -1499,7 +4345,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 73, "metadata": { "collapsed": false, "deletable": false, @@ -1511,7 +4357,69 @@ "solution": false } }, - "outputs": [], + "outputs": [ + { + "data": { + "text/html": [ + "
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s10s13
target_id
ENSMUST00000146665.2|ENSMUSG00000033845.13|OTTMUSG00000029329.3|OTTMUST00000072662.2|Mrpl15-004|Mrpl15|1569|UTR5:1-62|CDS:63-569|UTR3:570-1569|0.0000003.952259
ENSMUST00000134384.7|ENSMUSG00000025903.14|OTTMUSG00000021562.4|OTTMUST00000051163.2|Lypla1-002|Lypla1|1136|UTR5:1-126|CDS:127-801|UTR3:802-1136|0.2786692.769812
ENSMUST00000027036.10|ENSMUSG00000025903.14|OTTMUSG00000021562.4|OTTMUST00000051162.1|Lypla1-001|Lypla1|2507|UTR5:1-91|CDS:92-784|UTR3:785-2507|3.1747842.992448
ENSMUST00000081551.13|ENSMUSG00000033813.15|OTTMUSG00000042348.1|OTTMUST00000111602.1|Tcea1-001|Tcea1|2547|UTR5:1-100|CDS:101-1006|UTR3:1007-2547|6.9473511.058026
ENSMUST00000002533.14|ENSMUSG00000002459.17|OTTMUSG00000029338.4|OTTMUST00000072687.1|Rgs20-002|Rgs20|1778|UTR5:1-160|CDS:161-880|UTR3:881-1778|2.7950654.141637
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" + ], + "text/plain": [ + " s10 s13\n", + "target_id \n", + "ENSMUST00000146665.2|ENSMUSG00000033845.13|OTTM... 0.000000 3.952259\n", + "ENSMUST00000134384.7|ENSMUSG00000025903.14|OTTM... 0.278669 2.769812\n", + "ENSMUST00000027036.10|ENSMUSG00000025903.14|OTT... 3.174784 2.992448\n", + "ENSMUST00000081551.13|ENSMUSG00000033813.15|OTT... 6.947351 1.058026\n", + "ENSMUST00000002533.14|ENSMUSG00000002459.17|OTT... 2.795065 4.141637" + ] + }, + "execution_count": 73, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "kallisto_log2_tpm_expressed.head()" ] @@ -1536,7 +4444,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 74, "metadata": { "collapsed": false, "deletable": false, @@ -1548,7 +4456,28 @@ "solution": false } }, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "['ENSMUST00000146665.2',\n", + " 'ENSMUSG00000033845.13',\n", + " 'OTTMUSG00000029329.3',\n", + " 'OTTMUST00000072662.2',\n", + " 'Mrpl15-004',\n", + " 'Mrpl15',\n", + " '1569',\n", + " 'UTR5:1-62',\n", + " 'CDS:63-569',\n", + " 'UTR3:570-1569',\n", + " '']" + ] + }, + "execution_count": 74, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "s = 'ENSMUST00000146665.2|ENSMUSG00000033845.13|OTTMUSG00000029329.3|OTTMUST00000072662.2|Mrpl15-004|Mrpl15|1569|UTR5:1-62|CDS:63-569|UTR3:570-1569|'\n", "s.split('|')" @@ -1572,7 +4501,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 75, "metadata": { "collapsed": false, "deletable": false, @@ -1584,7 +4513,20 @@ "solution": false } }, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "array(['ENSMUSG00000033845.13', 'ENSMUSG00000025903.14',\n", + " 'ENSMUSG00000025903.14', ..., 'ENSMUSG00000064367.1',\n", + " 'ENSMUSG00000064368.1', 'ENSMUSG00000064370.1'], dtype=object)" + ] + }, + "execution_count": 75, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "kallisto_log2_tpm_expressed.index.map(lambda x: x.split('|')[1])" ] @@ -1607,7 +4549,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 76, "metadata": { "collapsed": false, "deletable": false, @@ -1619,7 +4561,70 @@ "solution": false } }, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "(9383, 2)\n" + ] + }, + { + "data": { + "text/html": [ + "
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s10s13
ENSMUSG00000033845.130.0000003.952259
ENSMUSG00000025903.140.2786692.769812
ENSMUSG00000025903.143.1747842.992448
ENSMUSG00000033813.156.9473511.058026
ENSMUSG00000002459.172.7950654.141637
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" + ], + "text/plain": [ + " s10 s13\n", + "ENSMUSG00000033845.13 0.000000 3.952259\n", + "ENSMUSG00000025903.14 0.278669 2.769812\n", + "ENSMUSG00000025903.14 3.174784 2.992448\n", + "ENSMUSG00000033813.15 6.947351 1.058026\n", + "ENSMUSG00000002459.17 2.795065 4.141637" + ] + }, + "execution_count": 76, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "kallisto_log2_tpm_expressed_genes = kallisto_log2_tpm_expressed.copy()\n", "kallisto_log2_tpm_expressed_genes.index = kallisto_log2_tpm_expressed.index.map(lambda x: x.split('|')[1])\n", @@ -1649,7 +4654,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 77, "metadata": { "collapsed": false, "deletable": false, @@ -1661,7 +4666,70 @@ "solution": false } }, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "(6733, 2)\n" + ] + }, + { + "data": { + "text/html": [ + "
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s10s13
ENSMUSG00000000001.40.2736516.259357
ENSMUSG00000000056.75.2181730.000000
ENSMUSG00000000058.611.6094940.344833
ENSMUSG00000000078.62.7237164.196505
ENSMUSG00000000085.160.0000005.360020
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" + ], + "text/plain": [ + " s10 s13\n", + "ENSMUSG00000000001.4 0.273651 6.259357\n", + "ENSMUSG00000000056.7 5.218173 0.000000\n", + "ENSMUSG00000000058.6 11.609494 0.344833\n", + "ENSMUSG00000000078.6 2.723716 4.196505\n", + "ENSMUSG00000000085.16 0.000000 5.360020" + ] + }, + "execution_count": 77, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "kallisto_log2_tpm_expressed_genes_summed = kallisto_log2_tpm_expressed_genes.groupby(level=0, axis=0).sum()\n", "print(kallisto_log2_tpm_expressed_genes_summed.shape)\n", @@ -1686,7 +4754,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 83, "metadata": { "collapsed": false, "deletable": false, @@ -1698,7 +4766,31 @@ "solution": false } }, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "before aligning: (6733,) (46983,)\n", + "after aligning: (46983,) (46983,)\n" + ] + }, + { + "data": { + "text/plain": [ + "ENSMUSG00000000001.4 0.273651\n", + "ENSMUSG00000000003.15 NaN\n", + "ENSMUSG00000000028.14 NaN\n", + "ENSMUSG00000000031.15 NaN\n", + "ENSMUSG00000000037.16 NaN\n", + "Name: s10, dtype: float64" + ] + }, + "execution_count": 83, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "x = kallisto_log2_tpm_expressed_genes_summed['s10']\n", "y = s10_featurecounts['log2_tpm']\n", @@ -1727,7 +4819,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 84, "metadata": { "collapsed": true, "deletable": false, @@ -1747,7 +4839,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 85, "metadata": { "collapsed": false, "deletable": false, @@ -1759,7 +4851,36 @@ "solution": false } }, - "outputs": [], + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/home/ucsd-train12/anaconda3/lib/python3.5/site-packages/matplotlib/__init__.py:892: UserWarning: axes.color_cycle is deprecated and replaced with axes.prop_cycle; please use the latter.\n", + " warnings.warn(self.msg_depr % (key, alt_key))\n" + ] + }, + { + "data": { + "text/plain": [ + "" + ] + }, + "execution_count": 85, + "metadata": {}, + "output_type": "execute_result" + }, + { + "data": { + "image/png": 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zmThX01UTWRsqxFSaNuNOTZkEpfXGmO8A34g8/gvgpdw1Sbzsld9ntMcZCK/n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\nufcow4ER7rrh7eP6fhGvUpVwa39ojPk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+ "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], "source": [ "sns.jointplot(x, y)" ] @@ -1782,7 +4903,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 86, "metadata": { "collapsed": false, "deletable": false, @@ -1794,7 +4915,36 @@ "solution": false } }, - "outputs": [], + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/home/ucsd-train12/anaconda3/lib/python3.5/site-packages/matplotlib/__init__.py:892: UserWarning: axes.color_cycle is deprecated and replaced with axes.prop_cycle; please use the latter.\n", + " warnings.warn(self.msg_depr % (key, alt_key))\n" + ] + }, + { + "data": { + "text/plain": [ + "" + ] + }, + "execution_count": 86, + "metadata": {}, + "output_type": "execute_result" + }, + { + "data": { + "image/png": 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dS0/f0JjNxLmarprI2lAhptK0GXdqyiQorTfG3A/cF3l8CfBc7pokXvbi3zLa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\n5t+rOw4wFBzmuotPHtf3i3iVqoRb+3N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+QXgtsscY4257UdyLtXYEWGqMaQQeMsYsZmzb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\nRDzj/weOIevDFLA/RwAAAABJRU5ErkJggg==\n", + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], "source": [ "sns.jointplot(x, y, stat_func=spearmanr)" ] @@ -1857,7 +5007,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 87, "metadata": { "collapsed": false, "deletable": false, @@ -1869,7 +5019,23 @@ "solution": false } }, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "ENSMUSG00000000001.4 -5.985706\n", + "ENSMUSG00000000056.7 5.218173\n", + "ENSMUSG00000000058.6 11.264661\n", + "ENSMUSG00000000078.6 -1.472789\n", + "ENSMUSG00000000085.16 -5.360020\n", + "dtype: float64" + ] + }, + "execution_count": 87, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "kallisto_diff = kallisto_log2_tpm_expressed_genes_summed['s10'] - kallisto_log2_tpm_expressed_genes_summed['s13']\n", "kallisto_diff.head()" @@ -1877,7 +5043,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 88, "metadata": { "collapsed": false, "deletable": false, @@ -1889,7 +5055,28 @@ "solution": false } }, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "" + ] + }, + "execution_count": 88, + "metadata": {}, + "output_type": "execute_result" + }, + { + "data": { + "image/png": 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SfmnuyWldriqSt2gwuPsscD/wHPAW8JS7HzSz+8zst3JtniHoqhwGHgd+O3f8ZeBp4FXg\nNSACfHElvhARgLGJpV2VVF8XIxaNkJxOr2RZIlUl1ByDuz8LWMmxx0se33+Rcx8GHr7UAkWW4sJV\nSXUkJxa/0igSidDWkmB0YkaTzyI5uvNZasrY5AwNiRh1i6ysWqirtYHUbJazWn5bBFAwSI0Zm5hZ\n8Iqk+eTvfj5xJrkSJYlUHQWD1JSxZIq2JQZDV1twk9uJIQWDCCgYpIakZzNMTqdDX5GUl18WY2Bo\nYiXKEqk6CgapGUtdJymvI7cshoaSRAIKBqkZc1ckLXJzW6l4LEprU5wBDSWJAAoGqQH5tY9OnT4H\nQF00M7cWUpZwl6C2N9cxlkwxMq4rk0RWdK0kkdUwOjrK3u8cYGg8eHxyaJwXXj7K0JlBmlvaaWlZ\n/Dk6WhL0n5mk//Q47S31K1uwSIVTj0FqQlNTM0SDX+htrcE6SI1N4TfeaW8OJqyPDY6tSH0i1UTB\nIDVjeiZY76g+sfQF8TpagmDoVzCIKBikdkzNBOsdNdQtPRjaW4IJa/UYRBQMUkOmcj2GhvqlT50l\n4lE6WxPqMYigYJAaMp3rMVzKUBJAz4ZmhkamSE6llrMskaqjYJCaMddjuMRg2Lw+mKzuPz2+bDWJ\nVCMFg9SMqZk08ViUWPTS3tY9uWA4ruEkWeMUDFIzJibTNDde+q05PRuaAQWDiIJBakJ+Ab2lrpNU\naPNcj0FDSbK2KRikJiSngvmFlsalraxaqK05QVtzguOn1WOQtU3BIDVhYiq4Immpm/SU2tLdyuDw\nBDOp2eUoS6QqhRqQNbPbgEcJguQJd39knjafB24HJoB73X1/7ng78JfA9UAG+E13f2l5yhcJzAXD\nJfYY8gvxbexI8FYWvO8UW7uDRZba2tqIRCLLVqtIpVu0x2BmUeAx4FZgF3C3mV1T0uZ24Cp3vxq4\nD/hCwac/Bzzj7tcCNwAHl6l2kTkXegyXFgzJ5Djf+vG7TCSD1VW/9eJRXnj5KHu/c4DR0dFlq1Ok\nGoTpMdwMHHL3owBm9hSwG3i7oM1u4EkAd3/JzNrNrBuYBH7G3e/NfS4N6KdMlt3EZH6O4dKHkhob\nm+lONAJnmZiJ0tzStkzViVSXMMHQAxwveNxPEBYLtRnIHZsFhszsSwS9hX3AA+4+eckVi8wj32No\nvcQeQ15+/+dzY1OXXZNItVrp/RjiwE3Ap919n5k9CvwB8NBCJ5nZnsXaiBSamEqTqIuSuIQF9Ao1\nN9ZRF49yblQb9khN6TOz0mMPu/ue+RqHCYYBYGvB497csdI2Wy7S5ri778t9/DTw+4u9YK7YPYXH\nzGw70BeiXlmDJqZmL+sehrxIJEJnaz1D56fIZMLt/iZSBXa4+5GwjcNcrvoKsNPMtplZArgL2FvS\nZi/w6wBmdgtw3t0H3X0QOG5mH8i1+zngQNjiRMJITqdJpTOXPPFcqqutgUw2y+jEzLI8n0i1WTQY\n3H0WuB94DngLeMrdD5rZfWb2W7k2zxB0VQ4DjwO/XfAU/xz4ipntJ5hn+FfL/DXIGnd2JBj2uZyb\n2wp1tjYEzzuqeQZZm0LNMbj7s4CVHHu85PH9Fzn3NeAjl1qgyGKGc7/Al2MoCaAzNwF9dnSK7vbG\nZXlOkWqiO5+l6p0dXd4ew7p29RhkbVMwSNUbzg8lLVOPobUpQV08yvCIgkHWJgWDVL3hfI9hmSaf\nI5EIXW0NnB+bYlZXJskapGCQqpcf8lmuoSQIhpMyWRid0DafsvYoGKTqDY9O05CIEo8t39u5qy2Y\nZzg3pktWZe1RMEhVy2azDI9M09ywvDfxr8tdjXRuXMEga4+CQara6MQMqXSGpmUPBvUYZO1SMEhV\n6z8dbMPZ1rS8wdBYH6epIc65Mc0xyNqjYJCq1ndiBLiwKupy6mprYGIqTXI6vezPLVLJFAxS1d4b\nyAVD6/Lcw1AoP5w0cHpi2Z9bpJIpGKSq9Z0YoS4Wob15+S5VzctPQB9XMMgao2CQqpWezXD01Bi9\n3S1Eo8u/J3P+ktX+MwoGWVsUDFK1Bk6Pk0pn2NbdsiLP39XWQAToOzG2Is8vUqkUDFK13stNPG/b\ntDLBUBePsq69nvdOjJGc0tVJsnYoGKRq5SeeV6rHANCzvpHZTJY3Dg+t2GuIVBoFg1St/KWqW7qb\nV+w1Nq8PJqBffefMir2GSKVRMEhVymazvDcwyhXrmmmsX96b2wptaK+nIRHjVT+9Yq8hUmkUDFKV\nhkemGEvOsKOnbUVfJxqNsGtHByeGJjg1rKuTZG1QMEhVyWazjIyM8OahEwBs7qpnZGSELCu3b8L1\nV3YBsF/DSbJGhOqDm9ltwKMEQfKEuz8yT5vPA7cDE8C97r6/4HNRYB/Q7+53LkfhsjaNjo6y9zsH\neLs/2Jzn/Ngk3/zBaZpb2mlZoTnoD17VCcCr75zmto9uX5kXEakgi/YYcr/UHwNuBXYBd5vZNSVt\nbgeucvergfuAL5Q8zQPAgWWpWNa8pqZmTpydJhqNcOWWDTQ2Na3o63V3NtLd1cRr75xhJjW7oq8l\nUgnCDCXdDBxy96PungKeAnaXtNkNPAng7i8B7WbWDWBmvcAdwF8uW9Wypk1MpRk6P0XPhmbq4rEV\nf71IJMInbtjMxFSavd9/b8VfT6TcwgRDD3C84HF/7thCbQYK2vwZ8HuwgoPAsqYMnJkEYNumlZ14\nhgtzGr/4U920NMb52vPOsYEzZLN6O0vtWrnr/AAz+yVg0N33m9mngFAL2pjZHuChFSxNqlj/UBKA\nbVesfDAkk+N868dn6epax67t7bx0cJh/89Wf8C9/6xba29tX/PVFlkmfmZUee9jd98zXOEwwDABb\nCx735o6VttkyT5t/AtxpZncAjUCrmT3p7r++0Avmii0q2My2A30h6pUalp7NcGJokvaWBB0ty78H\nw3waG5tpbmnjpmtbeWdgnL5TU+w/NMwnf6o4GLLZLKOjo+87v62tjUhk+Rf5E1mCHe5+JGzjMMHw\nCrDTzLYBJ4G7gLtL2uwFPg18zcxuAc67+yDwYO4/zOyTwO8uFgoiC/FjI6Rns6syjFQqGo3wDz/U\nwze+/x7/+j+9wTv9E/zTXzBam+pIz2Z53fv5xvcPE48niERg68YmyExz56euU+9CqsqiweDus2Z2\nP/AcFy5XPWhm9wFZd/+iuz9jZneY2WGCy1V/Y2XLlrVq/6FhYHXmF+bTu7GVO265glfePsve77/H\n3u+/R0MiRiaTZSadKWp7/Mw0v/DhDWWpU+RyhJpjcPdnASs59njJ4/sXeY7vAt9daoEiebOzGV46\ncIZ4LELPhpVbH2kxjfEUH74ywYmRRoZHZxifDLb+vKIhQ3dXMx0dHbz57hADZ8Y5ObxyC/yJrJQV\nnXwWWU4vvXWKs6PTXLO1lVisvDftt7a08PEdG4uOnR4cIBqtY/2GDtqaEzz97UPsP3ye/1VXMEmV\n0ZIYUjX++w+Daw+u2VqeYaSl6O5qYvsVbQyem+KtvvPlLkdkSRQMUhWOnhrl9cND7NrRQUdLotzl\nhPKR67oB+K/fO1LeQkSWSMEgVSHfW/iFj5TeW1m5NnY20d3ZgB8bYTw5U+5yREJTMEjFG59M8T/3\nHWdDZyM3fmBductZku7O4F4LP3auzJWIhKdgkIr3zR/1MTUzyy99bAexaHW9ZTd0NADw9hEFg1QP\nXZUkFSl/F/FMepavf+9dGutjfGxX14rvvbDcNnQEPYa3j54tcyUi4SkYpCLl913oH84wMj7D9Tva\n+dHrAwydGVzRvReWW0MixhXrGnnn2DlmM1liUS2NIZWvuvrlsqY0NjZx4OgY0UiED1/XQ3NL24rv\nvbASdva2k5xKc3xwrNyliISiYJCK1X9mkvPj03xgWwctjXXlLueSXd0b3Hfx9hENJ0l1UDBIxXqn\nP/gL+4ad1b3e0FwwaJ5BqoSCQSrS+fFp+s8k2dDZyPqOxnKXc1l6NjTTWB/XlUlSNRQMUpF+8Pog\n2Sxcu62r3KVctmg0gm3rZODMOGO60U2qgIJBKk42m+V7+08RjUa4emtHuctZFtfkAs6PqtcglU/B\nIBXHj53jxFCSbRubaEjUxhXV+YA73K8F9aTyKRik4rzw8jEAru5tLXMly2dnby4YjisYpPIpGKSi\npGcz/Oj1E3S2Jti0rqHc5Vy2bDbLyMgIsew0na0J/OhZRkZGgju4tU+DVKja6KdLzdj/zhnGkilu\n/ekeopHqv0s4mRznWz8+S1fXOlob4xw7nWTv997VXtBS0UIFg5ndBjzKhT2fH5mnzeeB2wn2fL7X\n3febWS/wJNANZIC/cPfPL1fxUnu+v38AgJ++biPHTtbGsEtjYzPNLW1csWGSY6eTjM/E2NhWvq1J\nRRaz6FCSmUWBx4BbgV3A3WZ2TUmb24Gr3P1q4D7gC7lPpYHfcfddwEeBT5eeK5IfbhkaPseLb5xg\nXVs9G1qzVbVYXhgbO4P7MU6fTZa5EpGFhZljuBk45O5H3T0FPAXsLmmzm6BngLu/BLSbWbe7n3L3\n/bnj48BBoHp2WpFVkV8w7z8+6ySnZ9nUVc+3fvgOU5PT5S5tWW3sDNZ5On1ussyViCwsTDD0AMcL\nHvfz/l/upW0GStuY2XbgQ8BLS65Sal5TUzPHh4IguPbK7qpcLG8xDfVx2poTnD6X1MSzVLRVuSrJ\nzFqAp4EHcj0HkSLp2Qx9J0ZpbUrMDbnUoo2djUzNzDI+mS53KSIXFWbyeQDYWvC4N3estM2W+dqY\nWZwgFL7s7l8PU5SZ7QEeCtNWasPx00lS6QwfvKqDSA1cjXQxGzqbONw/wvColsaQVdVnZqXHHnb3\nPfM1DhMMrwA7zWw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+ "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], "source": [ "sns.distplot(kallisto_diff)" ] @@ -1918,7 +5105,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 89, "metadata": { "collapsed": false, "deletable": false, @@ -1930,7 +5117,30 @@ "solution": false } }, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "(218,)\n" + ] + }, + { + "data": { + "text/plain": [ + "0 ENSMUSG00000000827.18\n", + "1 ENSMUSG00000001418.13\n", + "2 ENSMUSG00000002699.12\n", + "3 ENSMUSG00000002885.14\n", + "4 ENSMUSG00000002996.17\n", + "dtype: object" + ] + }, + "execution_count": 89, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "kallisto_s10_specific = kallisto_diff > (kallisto_diff.mean() + 2*kallisto_diff.std())\n", "kallisto_s10_specific_genes = pd.Series(kallisto_s10_specific.index[kallisto_s10_specific])\n", @@ -1960,7 +5170,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 95, "metadata": { "collapsed": false, "deletable": false, @@ -1972,17 +5182,41 @@ "solution": true } }, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "(162,)\n" + ] + }, + { + "data": { + "text/plain": [ + "0 ENSMUSG00000000386.14\n", + "1 ENSMUSG00000000399.10\n", + "2 ENSMUSG00000000581.8\n", + "3 ENSMUSG00000000753.15\n", + "4 ENSMUSG00000001127.12\n", + "dtype: object" + ] + }, + "execution_count": 95, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "# YOUR CODE HERE\n", - "\n", + "kallisto_s13_specific = kallisto_diff < (kallisto_diff.mean() - 2*kallisto_diff.std())\n", + "kallisto_s13_specific_genes = pd.Series(kallisto_s13_specific.index[kallisto_s13_specific])\n", "print(kallisto_s13_specific_genes.shape)\n", "kallisto_s13_specific_genes.head()\n" ] }, { "cell_type": "code", - "execution_count": null, + "execution_count": 96, "metadata": { "collapsed": true, "deletable": false, @@ -2022,7 +5256,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 97, "metadata": { "collapsed": false, "deletable": false, @@ -2034,7 +5268,23 @@ "solution": false } }, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "0 ENSMUSG00000000386\n", + "1 ENSMUSG00000000399\n", + "2 ENSMUSG00000000581\n", + "3 ENSMUSG00000000753\n", + "4 ENSMUSG00000001127\n", + "dtype: object" + ] + }, + "execution_count": 97, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "kallisto_s10_specific_genes_ensembl = kallisto_s10_specific_genes.map(lambda x: x.split('.')[0])\n", "kallisto_s13_specific_genes_ensembl = kallisto_s13_specific_genes.map(lambda x: x.split('.')[0])\n", @@ -2059,7 +5309,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 98, "metadata": { "collapsed": true, "deletable": false, @@ -2095,7 +5345,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 99, "metadata": { "collapsed": false, "deletable": false, @@ -2107,7 +5357,37 @@ "solution": false } }, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "==> kallisto_s10_specific_genes.csv <==\r\n", + "ENSMUSG00000000827\r\n", + "ENSMUSG00000001418\r\n", + "ENSMUSG00000002699\r\n", + "ENSMUSG00000002885\r\n", + "ENSMUSG00000002996\r\n", + "ENSMUSG00000003662\r\n", + "ENSMUSG00000003721\r\n", + "ENSMUSG00000004266\r\n", + "ENSMUSG00000004609\r\n", + "ENSMUSG00000004610\r\n", + "\r\n", + "==> kallisto_s13_specific_genes.csv <==\r\n", + "ENSMUSG00000000386\r\n", + "ENSMUSG00000000399\r\n", + "ENSMUSG00000000581\r\n", + "ENSMUSG00000000753\r\n", + "ENSMUSG00000001127\r\n", + "ENSMUSG00000001289\r\n", + "ENSMUSG00000001794\r\n", + "ENSMUSG00000002845\r\n", + "ENSMUSG00000004296\r\n", + "ENSMUSG00000004530\r\n" + ] + } + ], "source": [ "! head kallisto*specific_genes.csv" ] @@ -2136,9 +5416,9 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 101, "metadata": { - "collapsed": true, + "collapsed": false, "deletable": false, "nbgrader": { "checksum": "2bbd7ae0192d0c5b4e83790b66e4a732", @@ -2151,7 +5431,10 @@ }, "outputs": [], "source": [ - "# YOUR CODE HERE" + "# YOUR CODE HERE\n", + "#negative regulation of cellular metabolic processes\n", + "#regulation of macromolecule metabolic processes\n", + "#regulation of metabolic processes" ] }, { @@ -2179,7 +5462,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 107, "metadata": { "collapsed": false, "deletable": false, @@ -2191,16 +5474,163 @@ "solution": true } }, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "(46983, 9)\n" + ] + }, + { + "data": { + "text/html": [ + "
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ChrStartEndStrandLength/home/ucsd-train12/projects/shalek2013/processed_data/S13.Aligned.out.sorted.bamnew_columnfpkmtpm
Geneid
ENSMUSG00000102693.1chr130732533074322+107000NaNNaN
ENSMUSG00000064842.1chr131020163102125+11000NaNNaN
ENSMUSG00000051951.5chr1;chr1;chr13214482;3421702;36705523216968;3421901;3671498-;-;-363400NaNNaN
ENSMUSG00000102851.1chr132527573253236+48000NaNNaN
ENSMUSG00000103377.1chr133657313368549-281900NaNNaN
\n", + "
" + ], + "text/plain": [ + " Chr Start \\\n", + "Geneid \n", + "ENSMUSG00000102693.1 chr1 3073253 \n", + "ENSMUSG00000064842.1 chr1 3102016 \n", + "ENSMUSG00000051951.5 chr1;chr1;chr1 3214482;3421702;3670552 \n", + "ENSMUSG00000102851.1 chr1 3252757 \n", + "ENSMUSG00000103377.1 chr1 3365731 \n", + "\n", + " End Strand Length \\\n", + "Geneid \n", + "ENSMUSG00000102693.1 3074322 + 1070 \n", + "ENSMUSG00000064842.1 3102125 + 110 \n", + "ENSMUSG00000051951.5 3216968;3421901;3671498 -;-;- 3634 \n", + "ENSMUSG00000102851.1 3253236 + 480 \n", + "ENSMUSG00000103377.1 3368549 - 2819 \n", + "\n", + " /home/ucsd-train12/projects/shalek2013/processed_data/S13.Aligned.out.sorted.bam \\\n", + "Geneid \n", + "ENSMUSG00000102693.1 0 \n", + "ENSMUSG00000064842.1 0 \n", + "ENSMUSG00000051951.5 0 \n", + "ENSMUSG00000102851.1 0 \n", + "ENSMUSG00000103377.1 0 \n", + "\n", + " new_column fpkm tpm \n", + "Geneid \n", + "ENSMUSG00000102693.1 0 NaN NaN \n", + "ENSMUSG00000064842.1 0 NaN NaN \n", + "ENSMUSG00000051951.5 0 NaN NaN \n", + "ENSMUSG00000102851.1 0 NaN NaN \n", + "ENSMUSG00000103377.1 0 NaN NaN " + ] + }, + "execution_count": 107, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "# YOUR CODE HERE\n", + "s13_featurecounts = pd.read_table('s13_featureCounts.txt', skiprows=1, index_col=0)\n", + "reads = s13_featurecounts['/home/ucsd-train12/projects/shalek2013/processed_data/S13.Aligned.out.sorted.bam']\n", + "s13_featurecounts['new_column'] = (s13_featurecounts['Length'].sum() * reads)/2e3\n", + "s13_featurecounts['fpkm'] = (reads * 1e9)/(reads.sum() * s13_featurecounts.Length)\n", + "s13_featurecounts['tpm'] = (s13_featurecounts.fpkm * 1e6)/s13_featurecounts['fpkm'].sum()\n", "print(s13_featurecounts.shape)\n", "s13_featurecounts.head()" ] }, { "cell_type": "code", - "execution_count": null, + "execution_count": 108, "metadata": { "collapsed": false, "deletable": false, @@ -2213,7 +5643,19 @@ "solution": false } }, - "outputs": [], + "outputs": [ + { + "ename": "AssertionError", + "evalue": "", + "output_type": "error", + "traceback": [ + "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[1;31mAssertionError\u001b[0m Traceback (most recent call last)", + "\u001b[1;32m\u001b[0m in \u001b[0;36m\u001b[1;34m()\u001b[0m\n\u001b[1;32m----> 1\u001b[1;33m \u001b[1;32massert\u001b[0m \u001b[0mlen\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0ms13_featurecounts\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mcolumns\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mintersection\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;34m'fpkm'\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;34m'tpm'\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;34m'log2_tpm'\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m)\u001b[0m \u001b[1;33m==\u001b[0m \u001b[1;36m3\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 2\u001b[0m \u001b[1;32massert\u001b[0m \u001b[0ms13_featurecounts\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mloc\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;34m'ENSMUSG00000064370.1'\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;34m'log2_tpm'\u001b[0m\u001b[1;33m]\u001b[0m \u001b[1;33m==\u001b[0m \u001b[1;36m13.15202328657807\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n", + "\u001b[1;31mAssertionError\u001b[0m: " + ] + } + ], "source": [ "assert len(s13_featurecounts.columns.intersection(['fpkm', 'tpm', 'log2_tpm'])) == 3\n", "assert s13_featurecounts.loc['ENSMUSG00000064370.1', 'log2_tpm'] == 13.15202328657807" @@ -2274,7 +5716,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 109, "metadata": { "collapsed": false, "deletable": false, @@ -2284,11 +5726,34 @@ "grade_id": "ex14_answer", "locked": false, "solution": true - } + }, + "scrolled": true }, - "outputs": [], + "outputs": [ + { + "ename": "KeyError", + "evalue": "'log2_tpm'", + "output_type": "error", + "traceback": [ + "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[1;31mKeyError\u001b[0m Traceback (most recent call last)", + "\u001b[1;32m\u001b[0m in \u001b[0;36m\u001b[1;34m()\u001b[0m\n\u001b[0;32m 1\u001b[0m \u001b[1;31m# YOUR CODE HERE\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m----> 2\u001b[1;33m \u001b[0mfeaturecounts_diff\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0ms10_featurecounts\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;34m'log2_tpm'\u001b[0m\u001b[1;33m]\u001b[0m \u001b[1;33m-\u001b[0m \u001b[0ms13_featurecounts\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;34m'log2_tpm'\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 3\u001b[0m \u001b[0mprint\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mfeaturecounts_diff\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mshape\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 4\u001b[0m \u001b[0mfeaturecounts_diff\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mhead\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n", + "\u001b[1;32m/home/ucsd-train12/anaconda3/lib/python3.5/site-packages/pandas/core/frame.py\u001b[0m in \u001b[0;36m__getitem__\u001b[1;34m(self, key)\u001b[0m\n\u001b[0;32m 1967\u001b[0m \u001b[1;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m_getitem_multilevel\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mkey\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 1968\u001b[0m \u001b[1;32melse\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m-> 1969\u001b[1;33m \u001b[1;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m_getitem_column\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mkey\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 1970\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 1971\u001b[0m \u001b[1;32mdef\u001b[0m \u001b[0m_getitem_column\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mkey\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n", + "\u001b[1;32m/home/ucsd-train12/anaconda3/lib/python3.5/site-packages/pandas/core/frame.py\u001b[0m in \u001b[0;36m_getitem_column\u001b[1;34m(self, key)\u001b[0m\n\u001b[0;32m 1974\u001b[0m \u001b[1;31m# get column\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 1975\u001b[0m \u001b[1;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mcolumns\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mis_unique\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m-> 1976\u001b[1;33m \u001b[1;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m_get_item_cache\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mkey\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 1977\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 1978\u001b[0m \u001b[1;31m# duplicate columns & possible reduce dimensionality\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n", + "\u001b[1;32m/home/ucsd-train12/anaconda3/lib/python3.5/site-packages/pandas/core/generic.py\u001b[0m in \u001b[0;36m_get_item_cache\u001b[1;34m(self, item)\u001b[0m\n\u001b[0;32m 1089\u001b[0m \u001b[0mres\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mcache\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mget\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mitem\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 1090\u001b[0m \u001b[1;32mif\u001b[0m \u001b[0mres\u001b[0m \u001b[1;32mis\u001b[0m \u001b[1;32mNone\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m-> 1091\u001b[1;33m \u001b[0mvalues\u001b[0m \u001b[1;33m=\u001b[0m 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\u001b[0mnp\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0marange\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mlen\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mitems\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m[\u001b[0m\u001b[0misnull\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mitems\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n", + "\u001b[1;32m/home/ucsd-train12/anaconda3/lib/python3.5/site-packages/pandas/core/index.py\u001b[0m in \u001b[0;36mget_loc\u001b[1;34m(self, key, method, tolerance)\u001b[0m\n\u001b[0;32m 1757\u001b[0m 'backfill or nearest lookups')\n\u001b[0;32m 1758\u001b[0m \u001b[0mkey\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0m_values_from_object\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mkey\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m-> 1759\u001b[1;33m \u001b[1;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m_engine\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mget_loc\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mkey\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 1760\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 1761\u001b[0m indexer = self.get_indexer([key], method=method,\n", + "\u001b[1;32mpandas/index.pyx\u001b[0m in \u001b[0;36mpandas.index.IndexEngine.get_loc (pandas/index.c:3979)\u001b[1;34m()\u001b[0m\n", + "\u001b[1;32mpandas/index.pyx\u001b[0m in \u001b[0;36mpandas.index.IndexEngine.get_loc (pandas/index.c:3843)\u001b[1;34m()\u001b[0m\n", + "\u001b[1;32mpandas/hashtable.pyx\u001b[0m in \u001b[0;36mpandas.hashtable.PyObjectHashTable.get_item (pandas/hashtable.c:12265)\u001b[1;34m()\u001b[0m\n", + "\u001b[1;32mpandas/hashtable.pyx\u001b[0m in \u001b[0;36mpandas.hashtable.PyObjectHashTable.get_item (pandas/hashtable.c:12216)\u001b[1;34m()\u001b[0m\n", + "\u001b[1;31mKeyError\u001b[0m: 'log2_tpm'" + ] + } + ], "source": [ "# YOUR CODE HERE\n", + "featurecounts_diff = s10_featurecounts['log2_tpm'] - s13_featurecounts['log2_tpm']\n", "print(featurecounts_diff.shape)\n", "featurecounts_diff.head()" ] @@ -2428,6 +5893,10 @@ "outputs": [], "source": [ "# YOUR CODE HERE\n", + "kallisto_s10_specific = featurecounts_diff_nonzero < (kallisto_diff_nonzero.mean() - 2*kallisto_diff_nonzero.std())\n", + "kallisto_s10_specific_genes = pd.Series(kallisto_s10_specific.index[kallisto_s10_specific])\n", + "kallisto_s13_specific = featurecounts_diff_nonzero < (kallisto_diff_nonzero.mean() - 2*kallisto_diff_nonzero.std())\n", + "kallisto_s13_specific_genes = pd.Series(kallisto_s13_specific.index[kallisto_s13_specific])\n", "print('featurecounts_s10_specific_genes.shape', featurecounts_s10_specific_genes.shape)\n", "print('featurecounts_s13_specific_genes.shape', featurecounts_s13_specific_genes.shape)\n", "\n", @@ -2511,6 +5980,8 @@ "outputs": [], "source": [ "# YOUR CODE HERE\n", + "featurecounts_s10_specific_genes_ensembl = featurecounts_s10_specific_genes.index.map(lambda x: x.split('|')[1])\n", + "featurecounts_s13_specific_genes_ensembl = featurecounts_s13_specific_genes.index.map(lambda x: x.split('|')[1])\n", "featurecounts_s13_specific_genes_ensembl.head()" ] }, @@ -2619,4 +6090,4 @@ }, "nbformat": 4, "nbformat_minor": 0 -} \ No newline at end of file +}