biom262 · aguzikowski · Jan 19, 2016 · Jan 21, 2016 · Jan 26, 2016 · Feb 11, 2016
diff --git a/weeks/week01/7_tf_binding_promoters.ipynb b/weeks/week01/7_tf_binding_promoters.ipynb
diff --git a/weeks/week01/README.md b/weeks/week01/README.md
@@ -0,0 +1 @@
+x
diff --git a/weeks/week01/biom262-hw1 b/weeks/week01/biom262-hw1
diff --git a/weeks/week01/data/2 b/weeks/week01/data/2
@@ -0,0 +1 @@
+Hello I am a message in standard error (stderr)
diff --git a/weeks/week01/data/gencode.v19.annotation.chr22.transcript.promoter.nfkb.gtf b/weeks/week01/data/gencode.v19.annotation.chr22.transcript.promoter.nfkb.gtf
diff --git a/weeks/week03/.RData b/weeks/week03/.RData
diff --git a/weeks/week03/.Rhistory b/weeks/week03/.Rhistory
@@ -0,0 +1,18 @@
+lm <-read.table("littermates.txt",head=T)
+lm
+attach(lm)
+names(lm)
+mut
+mean (mut)
+medial (ctl)
+median(ctl)
+?median
+?read
+??read
+plot(lm)
+(q)
+()q
+[]q
+q
+quit
+q()
diff --git a/weeks/week03/R Practice in Class 1_19.ipynb b/weeks/week03/R Practice in Class 1_19.ipynb
diff --git a/weeks/week03/Rplots.pdf b/weeks/week03/Rplots.pdf
diff --git a/weeks/week03/Rplots1.pdf b/weeks/week03/Rplots1.pdf
diff --git a/weeks/week03/Rplots10.pdf b/weeks/week03/Rplots10.pdf
diff --git a/weeks/week03/Rplots11.pdf b/weeks/week03/Rplots11.pdf
diff --git a/weeks/week03/Rplots12.pdf b/weeks/week03/Rplots12.pdf
diff --git a/weeks/week03/Rplots13.pdf b/weeks/week03/Rplots13.pdf
diff --git a/weeks/week03/Rplots14.pdf b/weeks/week03/Rplots14.pdf
diff --git a/weeks/week03/Rplots15.pdf b/weeks/week03/Rplots15.pdf
diff --git a/weeks/week03/Rplots16.pdf b/weeks/week03/Rplots16.pdf
diff --git a/weeks/week03/Rplots17.pdf b/weeks/week03/Rplots17.pdf
diff --git a/weeks/week03/Rplots18.pdf b/weeks/week03/Rplots18.pdf
diff --git a/weeks/week03/Rplots2.pdf b/weeks/week03/Rplots2.pdf
diff --git a/weeks/week03/Rplots3.pdf b/weeks/week03/Rplots3.pdf
diff --git a/weeks/week03/Rplots4.pdf b/weeks/week03/Rplots4.pdf
diff --git a/weeks/week03/Rplots5.pdf b/weeks/week03/Rplots5.pdf
diff --git a/weeks/week03/Rplots6.pdf b/weeks/week03/Rplots6.pdf
diff --git a/weeks/week03/Rplots7.pdf b/weeks/week03/Rplots7.pdf
diff --git a/weeks/week03/Rplots8.pdf b/weeks/week03/Rplots8.pdf
diff --git a/weeks/week03/Rplots9.pdf b/weeks/week03/Rplots9.pdf
diff --git 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": 2,
    "metadata": {
     "collapsed": false,
     "deletable": false,
@@ -317,14 +328,25 @@
      "solution": false
     }
    },
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "73"
+      ]
+     },
+     "execution_count": 2,
+     "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 +392,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 4,
    "metadata": {
     "collapsed": false,
     "deletable": false,
@@ -378,7 +411,7 @@
        "0.000630957344480193"
       ]
      },
-     "execution_count": 3,
+     "execution_count": 4,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -389,7 +422,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 5,
    "metadata": {
     "collapsed": true,
     "deletable": false,
@@ -505,7 +538,7 @@
     }
    },
    "source": [
-    "YOUR ANSWER HERE"
+    "According to the gencode website, basic annotation \"identifies a subset of representative transcripts for each gene; prioritises full-length protein coding transcripts over partial or non-protein coding transcripts within the same gene, and intends to highlight those transcripts that will be useful to the majority of users.\" In contrats, the comprhensive annotation basically gives you all the information known about a gene including \"gene annotation on the reference chromosomes, scaffolds, assembly patches and alternate loci (haplotypes).\" The basic annotation is more straightforward but provides less information so I would want to use it if it provides information sufficient for the purpose of my study since it is more streamlined. "
    ]
   },
   {
@@ -857,7 +890,7 @@
     }
    },
    "source": [
-    "1. -S\n",
+    "1. -S (though may not be necessary since it's the default)\n",
     "2. -b\n",
     "3. -@ 4"
    ]
@@ -968,7 +1001,7 @@
     }
    },
    "source": [
-    "YOUR ANSWER HERE"
+    "If I were to use R or other programs I would use the tsv file. The h5 file would be used for kallisto's partner analysis software, sleuth."
    ]
   },
   {
@@ -1114,7 +1147,7 @@
     }
    },
    "source": [
-    "YOUR ANSWER HERE"
+    "The featurecounts file was made by summing up all of the transcripts that matched to a given annotation where as the kallisto files gives an estimated abundance for each transcript through their \"pseudoalignment\" approach"
    ]
   },
   {
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		Hello I am a message in standard error (stderr)