{
 "metadata": {
  "name": "Final Project"
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [
    {
     "cell_type": "heading",
     "level": 1,
     "metadata": {},
     "source": "Creating BAM files from Oly RNA-Seq data."
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "#Using the same methods we used Module 6 for De novo assembly I reran the Oly 106 female and the 106 male with a newly assembled\n#from Steven using TopHat and Trinity. Instead of the 10K contigs fasta I'm using the OlyO_Pat_v02 fasta. \nfrom IPython.display import Image\nImage(url='http://eagle.fish.washington.edu/dermochelys/Bioinformatics/iPlantAppTopHat2Setup3.jpg')",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "html": "<img src=\"http://eagle.fish.washington.edu/dermochelys/Bioinformatics/iPlantAppTopHat2Setup3.jpg\"/>",
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 1,
       "text": "<IPython.core.display.Image at 0x5112b70>"
      }
     ],
     "prompt_number": 1
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "#I then ran mpileup on both bam files generated to create SAM files. \nfrom IPython.display import Image\nImage(url='http://eagle.fish.washington.edu/dermochelys/Bioinformatics/iPlantAppmpileupSetup2.jpg')",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "html": "<img src=\"http://eagle.fish.washington.edu/dermochelys/Bioinformatics/iPlantAppmpileupSetup2.jpg\"/>",
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 2,
       "text": "<IPython.core.display.Image at 0x5112da0>"
      }
     ],
     "prompt_number": 2
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "#I created a new genome file using the OlyO_Pat_v02 fasta for IGV\nfrom IPython.display import Image\nImage(url='http://eagle.fish.washington.edu/dermochelys/Bioinformatics/IGVGenomebuild10Kcontigs.jpg')",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "html": "<img src=\"http://eagle.fish.washington.edu/dermochelys/Bioinformatics/IGVGenomebuild10Kcontigs.jpg\"/>",
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 3,
       "text": "<IPython.core.display.Image at 0x5112e80>"
      }
     ],
     "prompt_number": 3
    },
    {
     "cell_type": "heading",
     "level": 1,
     "metadata": {},
     "source": "Two BAMs and SAMs in IGV"
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "#I imported the bams and sams files for the olys and then overlayed them on top of each other. There is still very little coverage\n#but I have found some fun little differentially expressed areas. \nfrom IPython.display import Image\nImage(url='http://eagle.fish.washington.edu/dermochelys/Bioinformatics/IGVv02MFcompare1.jpg')",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "html": "<img src=\"http://eagle.fish.washington.edu/dermochelys/Bioinformatics/IGVv02MFcompare1.jpg\"/>",
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 4,
       "text": "<IPython.core.display.Image at 0x5112ef0>"
      }
     ],
     "prompt_number": 4
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "from IPython.display import Image\nImage(url='http://eagle.fish.washington.edu/dermochelys/Bioinformatics/IGVv02MFcompare2.jpg')",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "html": "<img src=\"http://eagle.fish.washington.edu/dermochelys/Bioinformatics/IGVv02MFcompare2.jpg\"/>",
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 8,
       "text": "<IPython.core.display.Image at 0x5112fd0>"
      }
     ],
     "prompt_number": 8
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "from IPython.display import Image\nImage(url='http://eagle.fish.washington.edu/dermochelys/Bioinformatics/IGVv02MFcompare3.jpg')",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "html": "<img src=\"http://eagle.fish.washington.edu/dermochelys/Bioinformatics/IGVv02MFcompare3.jpg\"/>",
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 7,
       "text": "<IPython.core.display.Image at 0x5112828>"
      }
     ],
     "prompt_number": 7
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "from IPython.display import Image\nImage(url='http://eagle.fish.washington.edu/dermochelys/Bioinformatics/IGVv02MFcompare4.jpg')",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "html": "<img src=\"http://eagle.fish.washington.edu/dermochelys/Bioinformatics/IGVv02MFcompare4.jpg\"/>",
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 6,
       "text": "<IPython.core.display.Image at 0x5112c88>"
      }
     ],
     "prompt_number": 6
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "from IPython.display import Image\nImage(url='http://eagle.fish.washington.edu/dermochelys/Bioinformatics/IGVv02MFcompare5.jpg')",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "html": "<img src=\"http://eagle.fish.washington.edu/dermochelys/Bioinformatics/IGVv02MFcompare5.jpg\"/>",
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 5,
       "text": "<IPython.core.display.Image at 0x5112e48>"
      }
     ],
     "prompt_number": 5
    },
    {
     "cell_type": "heading",
     "level": 1,
     "metadata": {},
     "source": "Comparing 2 males and 2 females in IGV"
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "from IPython.display import Image\nImage(url='http://eagle.fish.washington.edu/dermochelys/Bioinformatics/IGVv02MFcompare6.jpg')",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "html": "<img src=\"http://eagle.fish.washington.edu/dermochelys/Bioinformatics/IGVv02MFcompare6.jpg\"/>",
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 4,
       "text": "<IPython.core.display.Image at 0x5155eb8>"
      }
     ],
     "prompt_number": 4
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "from IPython.display import Image\nImage(url='http://eagle.fish.washington.edu/dermochelys/Bioinformatics/IGVv02MFcompare7.jpg')",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "html": "<img src=\"http://eagle.fish.washington.edu/dermochelys/Bioinformatics/IGVv02MFcompare7.jpg\"/>",
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 3,
       "text": "<IPython.core.display.Image at 0x5155e10>"
      }
     ],
     "prompt_number": 3
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "from IPython.display import Image\nImage(url='http://eagle.fish.washington.edu/dermochelys/Bioinformatics/IGVv02MFcompare8.jpg')",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "html": "<img src=\"http://eagle.fish.washington.edu/dermochelys/Bioinformatics/IGVv02MFcompare8.jpg\"/>",
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 2,
       "text": "<IPython.core.display.Image at 0x5155b38>"
      }
     ],
     "prompt_number": 2
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "from IPython.display import Image\nImage(url='http://eagle.fish.washington.edu/dermochelys/Bioinformatics/IGVv02MFcompare9.jpg')",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "html": "<img src=\"http://eagle.fish.washington.edu/dermochelys/Bioinformatics/IGVv02MFcompare9.jpg\"/>",
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 1,
       "text": "<IPython.core.display.Image at 0x5155be0>"
      }
     ],
     "prompt_number": 1
    },
    {
     "cell_type": "heading",
     "level": 1,
     "metadata": {},
     "source": "Gene Names from Transcriptome"
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "#Using the linux server I Blastn'd the new Oly scaffolding against the V2 transcriptome. Doing the Following.\n#wget oly scaffold\n#wget oly transcriptome\n#makeblastdb -in oly scaffold fasta -dbtype nucl -out Olyv02\n#blastn -query olytrans fasta -db olyscaffold -out olytrans2olyscaf.tab -evalue 1E-20 -matchs_per_seq 1 -outfmt 6",
     "language": "python",
     "metadata": {},
     "outputs": []
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "#after install BioPerl onto the linux server I downloaded the blast2gff.pl script. This was run on the blast output using this script:\n#perl blast2gff.pl --blast_result_file ~/BLAST/bin/olyblast/OlyTrans2OlyScaf.tab \n#--reference_sequence_file ~/BLAST/bin/olyblast/OlyO_Pat_v02.fa \n#--gff_output_file ~/BLAST/bin/olyblast/Olyv02.gff ",
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 1
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "#After importing this file into IGV I get a blue line. I have no idea what this means. \nfrom IPython.display import Image\nImage(url='http://eagle.fish.washington.edu/dermochelys/Bioinformatics/IGVv02MFcompare10.jpg')",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "html": "<img src=\"http://eagle.fish.washington.edu/dermochelys/Bioinformatics/IGVv02MFcompare10.jpg\"/>",
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 2,
       "text": "<IPython.core.display.Image at 0x5148ba8>"
      }
     ],
     "prompt_number": 2
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "#Also I have been running the LARVAE through top hat but I don't show them here as I'm trying to do the gff stuff today. ",
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 3
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "",
     "language": "python",
     "metadata": {},
     "outputs": []
    }
   ],
   "metadata": {}
  }
 ]
}