updated notebooks with information about project progress for pre

release
yaaminiv · Nov 5, 2016 · 121d738 · 121d738
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diff --git a/notebooks/.ipynb_checkpoints/2016-10-28-oly-gonad-OA-part-2-BLAST-checkpoint.ipynb b/notebooks/.ipynb_checkpoints/2016-10-28-oly-gonad-OA-part-2-BLAST-checkpoint.ipynb
@@ -22,8 +22,54 @@
     "\n",
     "The Uniprot database was downloaded on 2016-10-28 from this url: http://www.uniprot.org/uniprot/?query=&fil=reviewed%3Ayes&columns=id%2Centry%20name%2Creviewed%2Cprotein%20names%2Cgenes%2Corganism%2Clength%2Cgo(biological%20process)%2Cgo-id%2Ccomment(PATHWAY)%2Cdatabase(UniPathway)%2Cdatabase(CDD)%2Cdatabase(Pfam). \n",
     "\n",
-    "It includes Uniprot codes, protein names, gene names, organism information, sequence length, gene ontology, UniPathway, CDD and Pfam data.\n",
-    "\n",
+    "It includes Uniprot codes, protein names, gene names, organism information, sequence length, gene ontology, UniPathway, CDD and Pfam data. Before I begin, I will set my working directory in a way that will allow me to work from a remote machine if needed."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "'/Users/yaaminivenkataraman/Documents/School/Year1/FISH-546/yaaminiv-fish546-2016/notebooks'"
+      ]
+     },
+     "execution_count": 2,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "pwd"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "/Users/yaaminivenkataraman/Documents/School/Year1/FISH-546/yaaminiv-fish546-2016\n"
+     ]
+    }
+   ],
+   "source": [
+    "cd /Users/yaaminivenkataraman/Documents/School/Year1/FISH-546/yaaminiv-fish546-2016"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
     "The first step involves acquiring the .fasta file and setting it as my database. To do this, I will use the following code:\n",
     "\n",
     "1. use `makeblastdb` to create the database that we need\n",
@@ -232345,6 +232391,15 @@
     "-outfmt 6"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "collapsed": true
+   },
+   "source": [
+    "It seems like my blastx is not running to completion because of my jupyter notebook websockets timing out. I will try running this analysis in the command line, and hope to have an interpretation of this blastx by 2016-11-07."
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,

diff --git a/notebooks/.ipynb_checkpoints/2016-11-04-oly-gonad-OA-part3-kallisto-checkpoint.ipynb b/notebooks/.ipynb_checkpoints/2016-11-04-oly-gonad-OA-part3-kallisto-checkpoint.ipynb
@@ -125,16 +125,18 @@
     "2. `-i` indicates when index to use\n",
     "3. `-o` tells the program where to write the output\n",
     "4. `--single` allows me to process single-end reads\n",
-    "5. `-l` estimated average fragment length\n",
+    "5. `-l` estimated average fragment length from [FastQC output](https://github.com/yaaminiv/yaaminiv-fish546-2016/blob/master/notebooks/2016-10-19-oly-gonad-OA-part-1-FASTQC-results.ipynb)\n",
     "6. `-s` estimated standard deviation of fragment length\n",
     "7. fastq file to be used\n",
     "\n",
-    "**1. filtered_106A_Female_Mix_GATCAG_L004_R1.fastq**"
+    "**1. filtered_106A_Female_Mix_GATCAG_L004_R1.fastq**\n",
+    "\n",
+    "### NOTE: As of 2016-11-04, I stopped here because I'm trying to figure out how to find `-s` for my .fastq files. I will complete this analysis by 2016-11-07."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 3,
    "metadata": {
     "collapsed": false
    },
@@ -144,6 +146,8 @@
      "output_type": "stream",
      "text": [
       "\r\n",
+      "Error: Missing read files\r\n",
+      "Error: cannot supply mean/sd without supplying both -l and -s\r\n",
       "Error: fragment length mean and sd must be supplied for single-end reads using -l and -s\r\n",
       "\r\n",
       "Usage: kallisto quant [arguments] FASTQ-files\r\n",
@@ -174,8 +178,8 @@
     "-i /Users/yaaminivenkataraman/Documents/School/Year1/FISH-546/yaaminiv-fish546-2016/data/kallisto-index-OlyO-v6 \\\n",
     "-o /Users/yaaminivenkataraman/Documents/School/Year1/FISH-546/yaaminiv-fish546-2016/analyses \\\n",
     "--single \\\n",
-    "-l \\\n",
-    "-s \\\n",
+    "-l 76 \\\n",
+    "-s \\ #I'm still trying to figure out where to get this number from!\n",
     "/Users/yaaminivenkataraman/Documents/School/Year1/FISH-546/yaaminiv-fish546-2016/data/filtered_106A_Female_Mix_GATCAG_L004_R1.fastq"
    ]
   },

diff --git a/notebooks/2016-10-28-oly-gonad-OA-part-2-BLAST.ipynb b/notebooks/2016-10-28-oly-gonad-OA-part-2-BLAST.ipynb
@@ -22,8 +22,54 @@
     "\n",
     "The Uniprot database was downloaded on 2016-10-28 from this url: http://www.uniprot.org/uniprot/?query=&fil=reviewed%3Ayes&columns=id%2Centry%20name%2Creviewed%2Cprotein%20names%2Cgenes%2Corganism%2Clength%2Cgo(biological%20process)%2Cgo-id%2Ccomment(PATHWAY)%2Cdatabase(UniPathway)%2Cdatabase(CDD)%2Cdatabase(Pfam). \n",
     "\n",
-    "It includes Uniprot codes, protein names, gene names, organism information, sequence length, gene ontology, UniPathway, CDD and Pfam data.\n",
-    "\n",
+    "It includes Uniprot codes, protein names, gene names, organism information, sequence length, gene ontology, UniPathway, CDD and Pfam data. Before I begin, I will set my working directory in a way that will allow me to work from a remote machine if needed."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "'/Users/yaaminivenkataraman/Documents/School/Year1/FISH-546/yaaminiv-fish546-2016/notebooks'"
+      ]
+     },
+     "execution_count": 2,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "pwd"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "/Users/yaaminivenkataraman/Documents/School/Year1/FISH-546/yaaminiv-fish546-2016\n"
+     ]
+    }
+   ],
+   "source": [
+    "cd /Users/yaaminivenkataraman/Documents/School/Year1/FISH-546/yaaminiv-fish546-2016"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
     "The first step involves acquiring the .fasta file and setting it as my database. To do this, I will use the following code:\n",
     "\n",
     "1. use `makeblastdb` to create the database that we need\n",
@@ -232346,17 +232392,12 @@
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": null,
+   "cell_type": "markdown",
    "metadata": {
     "collapsed": true
    },
-   "outputs": [],
    "source": [
-    "!/Applications/ncbi-blast-2.5.0+/bin/blastx \\\n",
-    "-query /Users/yaaminivenkataraman/Documents/School/Year1/FISH-546/yaaminiv-fish546-2016/data/OlyO_v6_transcriptome.fa \\\n",
-    "-db /Users/yaaminivenkataraman/Documents/School/Year1/FISH-546/yaaminiv-fish546-2016/data/uniprot-all \\\n",
-    "-outfmt 6"
+    "It seems like my blastx is not running to completion because of my jupyter notebook websockets timing out. I will try running this analysis in the command line, and hope to have an interpretation of this blastx by 2016-11-07."
    ]
   },
   {

diff --git a/notebooks/2016-11-04-oly-gonad-OA-part3-kallisto.ipynb b/notebooks/2016-11-04-oly-gonad-OA-part3-kallisto.ipynb
@@ -125,16 +125,18 @@
     "2. `-i` indicates when index to use\n",
     "3. `-o` tells the program where to write the output\n",
     "4. `--single` allows me to process single-end reads\n",
-    "5. `-l` estimated average fragment length\n",
+    "5. `-l` estimated average fragment length from [FastQC output](https://github.com/yaaminiv/yaaminiv-fish546-2016/blob/master/notebooks/2016-10-19-oly-gonad-OA-part-1-FASTQC-results.ipynb)\n",
     "6. `-s` estimated standard deviation of fragment length\n",
     "7. fastq file to be used\n",
     "\n",
-    "**1. filtered_106A_Female_Mix_GATCAG_L004_R1.fastq**"
+    "**1. filtered_106A_Female_Mix_GATCAG_L004_R1.fastq**\n",
+    "\n",
+    "### NOTE: As of 2016-11-04, I stopped here because I'm trying to figure out how to find `-s` for my .fastq files. I will complete this analysis by 2016-11-07."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 3,
    "metadata": {
     "collapsed": false
    },
@@ -144,6 +146,8 @@
      "output_type": "stream",
      "text": [
       "\r\n",
+      "Error: Missing read files\r\n",
+      "Error: cannot supply mean/sd without supplying both -l and -s\r\n",
       "Error: fragment length mean and sd must be supplied for single-end reads using -l and -s\r\n",
       "\r\n",
       "Usage: kallisto quant [arguments] FASTQ-files\r\n",
@@ -174,8 +178,8 @@
     "-i /Users/yaaminivenkataraman/Documents/School/Year1/FISH-546/yaaminiv-fish546-2016/data/kallisto-index-OlyO-v6 \\\n",
     "-o /Users/yaaminivenkataraman/Documents/School/Year1/FISH-546/yaaminiv-fish546-2016/analyses \\\n",
     "--single \\\n",
-    "-l \\\n",
-    "-s \\\n",
+    "-l 76 \\\n",
+    "-s \\ #I'm still trying to figure out where to get this number from!\n",
     "/Users/yaaminivenkataraman/Documents/School/Year1/FISH-546/yaaminiv-fish546-2016/data/filtered_106A_Female_Mix_GATCAG_L004_R1.fastq"
    ]
   },