Week04

weeks/week04/0_alignment_expression_quantification.ipynb

@@ -270,7 +270,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 4,
    "metadata": {
     "collapsed": false,
     "deletable": false,
@@ -282,7 +282,18 @@
      "solution": false
     }
    },
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "25"
+      ]
+     },
+     "execution_count": 4,
+     "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": [
+       "65"
+      ]
+     },
+     "execution_count": 2,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
-    "ord('I')"
+    "ord('A')"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 8,
    "metadata": {
     "collapsed": false,
     "deletable": false,
@@ -336,7 +358,18 @@
      "solution": false
     }
    },
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "33"
+      ]
+     },
+     "execution_count": 8,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "ord('!')"
    ]
@@ -359,7 +392,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 14,
    "metadata": {
     "collapsed": false,
     "deletable": false,
@@ -369,7 +402,8 @@
      "grade_id": "5_fastq_their_answer",
      "locked": false,
      "solution": true
-    }
+    },
+    "scrolled": true
    },
    "outputs": [
     {
@@ -378,20 +412,23 @@
        "0.000630957344480193"
       ]
      },
-     "execution_count": 3,
+     "execution_count": 14,
      "metadata": {},
      "output_type": "execute_result"
     }
    ],
    "source": [
-    "10**(-(ord(\"A\") - ord(\"!\"))/10)"
+    "# The ordinal line in wikipedia and the 1.8+ standard are related by subtracting 33 \n",
+    "# from the ordinal this is totally not clear from the wikipedia page\n",
+    "p = 10**(-32/10)\n",
+    "p"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 16,
    "metadata": {
-    "collapsed": true,
+    "collapsed": false,
     "deletable": false,
     "nbgrader": {
      "checksum": "897dd4b038a302492821d9932eda240e",
@@ -505,7 +542,7 @@
     }
    },
    "source": [
-    "YOUR ANSWER HERE"
+    "If you were looking for something that is not an annotated event (like an alternative polyA selection, intron retention, etc.) aside from simple changes in the expression of common and well annotated transcripts, use the comprehensive annotation. If you are only interested in the \"standard\" sorts of changes, then shrinking the \"mapping space\" could increase your ability to accurately detect the types of changes you are looking for (by reducing mapping to things that are presumably not there or that you don't care about)."
    ]
   },
   {
@@ -811,8 +848,11 @@
     }
    },
    "source": [
-    "1. S10.Log.final.out\n",
-    "2. S10.Log.out"
+    "for all the stats:\n",
+    "[ucsd-train03@tscc-login1 processed_data]$ less S10.Log.final.out \n",
+    "\n",
+    "for all the settings:\n",
+    "[ucsd-train03@tscc-login1 processed_data]$ less S10.Log.out "
    ]
   },
   {
@@ -857,9 +897,9 @@
     }
    },
    "source": [
-    "1. -S\n",
-    "2. -b\n",
-    "3. -@ 4"
+    "1: samtools view --input-fmt-option OPT=SAM\n",
+    "2: samtools view --output-fmt FORMAT[,OPT[BAM]]\n",
+    "3: samtools sort -@, --threads INT"
    ]
   },
   {
@@ -968,7 +1008,7 @@
     }
    },
    "source": [
-    "YOUR ANSWER HERE"
+    "The .json file seems to contain the parameters used in kallisto. The .h5 file is not readable with head and tail commands, and would be used with sleuth. The .tsv file is clearly the data you would want for use in R and other programs. "
    ]
   },
   {
@@ -1007,9 +1047,12 @@
     }
    },
    "source": [
-    "1. -s\n",
-    "2. -B\n",
-    "3. --primary"
+    "1)\n",
+    "    -s <int>           \"Perform strand-specific read counting. Possible values: 0 (unstranded), 1 (stranded) and 2 (reversely stranded). 0 by default.\"\n",
+    "                      \n",
+    "2) -B\n",
+    "\n",
+    "3) --primary"
    ]
   },
   {
@@ -1114,7 +1157,7 @@
     }
    },
    "source": [
-    "YOUR ANSWER HERE"
+    "I am probably wrong, but it seems like featureCounts.txt doesn't actually count anything, it only lists the various mapped features. The .tsv file seems to give you a count estimate for each feature, collapsing aligned features."
    ]
   },
   {