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": 1,
    "metadata": {
     "collapsed": false,
     "deletable": false,
@@ -317,14 +328,25 @@
      "solution": false
     }
    },
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "73"
+      ]
+     },
+     "execution_count": 1,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "ord('I')"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "metadata": {
     "collapsed": false,
     "deletable": false,
@@ -336,7 +358,18 @@
      "solution": false
     }
    },
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "33"
+      ]
+     },
+     "execution_count": 2,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "ord('!')"
    ]
@@ -354,12 +387,18 @@
     }
    },
    "source": [
-    "Use Python to write code to find the probability of incorrect mapping corresponding to the letter \"A\""
+    "Use Python to write code to find the probability of incorrect mapping corresponding to the letter \"A\"\n",
+    "\n",
+    "$ Q = -10 \\log_{10} p$"
    ]
   },
   {
    "cell_type": "code",
+<<<<<<< HEAD
+   "execution_count": 5,
+=======
    "execution_count": 3,
+>>>>>>> 4e1a84a633f245aaea96eb706d9feeef27fd7bfa
    "metadata": {
     "collapsed": false,
     "deletable": false,
@@ -371,25 +410,62 @@
      "solution": true
     }
    },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+<<<<<<< HEAD
+       "65"
+      ]
+     },
+     "execution_count": 5,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "ord(\"A\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "metadata": {
+    "collapsed": false
+   },
    "outputs": [
     {
      "data": {
       "text/plain": [
        "0.000630957344480193"
       ]
      },
+     "execution_count": 9,
+=======
+       "0.000630957344480193"
+      ]
+     },
      "execution_count": 3,
+>>>>>>> 4e1a84a633f245aaea96eb706d9feeef27fd7bfa
      "metadata": {},
      "output_type": "execute_result"
     }
    ],
    "source": [
+<<<<<<< HEAD
+    "10**((ord(\"A\")-33)/(-10))"
+=======
     "10**(-(ord(\"A\") - ord(\"!\"))/10)"
+>>>>>>> 4e1a84a633f245aaea96eb706d9feeef27fd7bfa
    ]
   },
   {
    "cell_type": "code",
+<<<<<<< HEAD
+   "execution_count": 10,
+=======
    "execution_count": 4,
+>>>>>>> 4e1a84a633f245aaea96eb706d9feeef27fd7bfa
    "metadata": {
     "collapsed": true,
     "deletable": false,
@@ -466,7 +542,11 @@
     }
    },
    "source": [
+<<<<<<< HEAD
+    "You would use the flag outReadsUnmapped and use the argument fastx."
+=======
     "--outReadsUnmapped Fastx"
+>>>>>>> 4e1a84a633f245aaea96eb706d9feeef27fd7bfa
    ]
   },
   {
@@ -505,7 +585,9 @@
     }
    },
    "source": [
-    "YOUR ANSWER HERE"
+    "You would use the comprehensive annotation when you are interested in a complete annotation of every transcript that has been annotated. If you are only interested in the protein coding transcripts that are a subset of the comprehensive annotation, you would use the basic annoation. \n",
+    "\n",
+    "So biologically, I would use the basic annotation if I am interested in how the level of a particular mRNA expression is changing. I would use complete when I am not sure what to expect in my alignment and I want to see all the places where my reads align. "
    ]
   },
   {
@@ -697,7 +779,13 @@
     }
    },
    "source": [
+<<<<<<< HEAD
+    "With single end reads you have to specify the average read length as determined from the bioanalyzer. \n",
+    "\n",
+    "--single --fragment-length 190"
+=======
     "--single --fragment-length=200.1"
+>>>>>>> 4e1a84a633f245aaea96eb706d9feeef27fd7bfa
    ]
   },
   {
@@ -811,8 +899,13 @@
     }
    },
    "source": [
+<<<<<<< HEAD
+    "1) Log.final.out\n",
+    "2) Log.out"
+=======
     "1. S10.Log.final.out\n",
     "2. S10.Log.out"
+>>>>>>> 4e1a84a633f245aaea96eb706d9feeef27fd7bfa
    ]
   },
   {
@@ -857,9 +950,15 @@
     }
    },
    "source": [
+<<<<<<< HEAD
+    "1) samtools view it will already recognize that the input is SAM\n",
+    "2) if you want to output to bam, the the flag -b \n",
+    "3) -@ allows you to specify how many threads and processors to use"
+=======
     "1. -S\n",
     "2. -b\n",
     "3. -@ 4"
+>>>>>>> 4e1a84a633f245aaea96eb706d9feeef27fd7bfa
    ]
   },
   {
@@ -968,7 +1067,7 @@
     }
    },
    "source": [
-    "YOUR ANSWER HERE"
+    "The tsv file is used to read the quantification into other programs. The json file provides a log of how the program ran without actually giving the quantifications."
    ]
   },
   {
@@ -1007,9 +1106,15 @@
     }
    },
    "source": [
+<<<<<<< HEAD
+    "1) -s\n",
+    "2) -B\n",
+    "3) --primary"
+=======
     "1. -s\n",
     "2. -B\n",
     "3. --primary"
+>>>>>>> 4e1a84a633f245aaea96eb706d9feeef27fd7bfa
    ]
   },
   {