{
 "metadata": {
  "name": "Larvae_Overrepresented_Sequences"
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [
    {
     "cell_type": "heading",
     "level": 4,
     "metadata": {},
     "source": "List of overrepresented sequences from Bisulfite Sequencing run with Larvae files.  This entry lists the possible source, sequence, and percentage of possible overrepresented sequences/adapters."
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": "From November Run:"
    },
    {
     "cell_type": "raw",
     "metadata": {},
     "source": "F R1:\nTruSeq Adapter, Index 3 (100% over 50bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGC (1.02%)\nNo Hit AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG (0.67%)\nTruSeq Adapter, Index 3 (100% over 50bp) ATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCC (0.47%)\nNo Hit GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA (0.20%)\n\nF R2:\nIllumina Single End PCR Primer 1 (100% over 50bp) GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG (1.03%)\nNo Hit TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC (0.31%)\nIllumina Single End PCR Primer 1 (100% over 50bp) ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT (0.28%)\nIllumina Single End PCR Primer 1 (98% over 50bp) ATCGGAAGAGCGTCGTGTAGGGAAAGAGGGTAGATCTCGGTGGTCGCCGT (0.12%)\nNo Hit ACTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC (0.10%)\n\nT3D3 R1:\nTruSeq Adapter, Index 6 (100% over 50bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGC (1.97%)\nTruSeq Adapter, Index 6 (100% over 50bp) ATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCC (0.65%)\n\nT3D3 R2:\nIllumina Single End PCR Primer 1 (100% over 50bp) GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG (2.02%)\nIllumina Single End PCR Primer 1 (100% over 50bp) ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT (0.40%)\nIllumina Single End PCR Primer 1 (98% over 50bp) ATCGGAAGAGCGTCGTGTAGGGAAAGAGGGTAGATCTCGGTGGTCGCCGT (0.15%)\n\nT1D3 R1:\nTruSeq Adapter, Index 4 (100% over 50bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGC (1.48%)\nTruSeq Adapter, Index 4 (100% over 50bp) ATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGCC (0.23%)\n\nT1D3 R2:\nIllumina Single End PCR Primer 1 (100% over 50bp) GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG (1.51%)\nIllumina Single End PCR Primer 1 (100% over 50bp) ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT (0.15%)\n\nT1D5 R1:\nTruSeq Adapter, Index 5 (100% over 50bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGC (0.60%)\nTruSeq Adapter, Index 5 (100% over 50bp) ATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCC (0.25%)\n\nT1D5 R2:\nIllumina Single End PCR Primer 1 (100% over 50bp) GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG (0.62%)\nIllumina Single End PCR Primer 1 (100% over 50bp) ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT (0.17%)\n\nT3D5 R1:\nTruSeq Adapter, Index 7 (100% over 50bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGC (1.23%)\nTruSeq Adapter, Index 7 (100% over 50bp) ATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCC (0.19%)\n\nT3D5 R2:\nIllumina Single End PCR Primer 1 (100% over 50bp) GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG (1.28%)\nIllumina Single End PCR Primer 1 (100% over 50bp) ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT (0.19%)\n\nM1 R1:\nTruSeq Adapter, Index 8 (100% over 50bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGC (1.39%)\nTruSeq Adapter, Index 8 (100% over 50bp) ATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGCC (0.44%)\n\nM1 R2:\nIllumina Single End PCR Primer 1 (100% over 50bp) GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG (1.41%)\nIllumina Single End PCR Primer 1 (100% over 50bp) ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT (0.26%)\nIllumina Single End PCR Primer 1 (98% over 50bp) ATCGGAAGAGCGTCGTGTAGGGAAAGAGGGTAGATCTCGGTGGTCGCCGT (0.11%)\n\nM3 R1:\nTruSeq Adapter, Index 9 (100% over 50bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGATCTCGTATGC (0.75%)\n\nM3 R2:\nIllumina Single End PCR Primer 1 (100% over 50bp) GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG (0.65%)"
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": "From September Run:"
    },
    {
     "cell_type": "raw",
     "metadata": {},
     "source": "F R1:\nNo Hit AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG (1.00%)\nNo Hit GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA (0.29%)\nTruSeq Adapter, Index 3 (100% over 50bp) ATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCC (0.21%)\nTruSeq Adapter, Index 3 (100% over 50bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGC (0.18%)\nNo Hit TGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG (0.13%)\n\nF R2:\nNo Hit TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC (0.36%)\nNo Hit ACTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC (0.11%)\n\nT3D3 R1:\nTruSeq Adapter, Index 6 (100% over 50bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGC (0.73%)\nTruSeq Adapter, Index 6 (100% over 50bp) ATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCC (0.35%)\n\nT3D3 R2:\nNo overrepresented sequences\n\nT1D3 R1:\nTruSeq Adapter, Index 4 (100% over 50bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGC (0.35%)\n\nT1D3 R2:\nNo overrepresented sequences\n\nT1D5 R1:\nTruSeq Adapter, Index 5 (100% over 50bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGC (0.20%)\nTruSeq Adapter, Index 5 (100% over 50bp) ATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCC (0.13%)\n\nT1D5 R2:\nNo overrepresented sequences\n\nT3D5 R1:\nTruSeq Adapter, Index 7 (100% over 50bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGC (0.52%)\nTruSeq Adapter, Index 7 (100% over 50bp) ATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCC (0.12%)\n\nT3D5 R2:\nNo overrepresented sequences\n\nM1 R1:\nTruSeq Adapter, Index 8 (100% over 50bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGC (0.38%)\nTruSeq Adapter, Index 8 (100% over 50bp) ATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGCC (0.21%)\n\nM1 R2:\nNo overrepresented sequences\n\nM3 R1:\nTruSeq Adapter, Index 9 (100% over 50bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGATCTCGTATGC (0.33%)\n\nM3 R2:\nNo overrepresented sequences"
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "#NOTEBOOK NAME\nnb='Larvae_Overrepresented_Sequences'\n\n#NOTEBOOK LOCATION\nnbloc='/Users/claireolson/Dropbox/Lab\\ \\(1\\)/IPython_nbs/Claire/'\n\n\n\n#TIMESTAMP\ndate=!date +%m%d_%H%M\n#LOCATION OF POST DIRECTORY\npost='/Volumes/web/Mollusk/iPython_Posts/'",
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 3
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "cd {post}",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": "/Volumes/web/Mollusk/iPython_Posts\n"
      }
     ],
     "prompt_number": 4
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "!ipython nbconvert {nbloc}{nb} --to html --template full --output {nb}{date}",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": "[NbConvertApp] Using existing profile dir: u'/Users/claireolson/.ipython/profile_default'\r\n"
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": "[NbConvertApp] Converting notebook /Users/claireolson/Dropbox/Lab (1)/IPython_nbs/Claire/Larvae_Overrepresented_Sequences.ipynb to html\r\n[NbConvertApp] Support files will be in Larvae_Overrepresented_Sequences[0331_1500]_files/\r\n"
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": "[NbConvertApp] Loaded template html_full.tpl\r\n"
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": "[NbConvertApp] Writing 202868 bytes to Larvae_Overrepresented_Sequences[0331_1500].html\r\n"
      }
     ],
     "prompt_number": 5
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "",
     "language": "python",
     "metadata": {},
     "outputs": []
    }
   ],
   "metadata": {}
  }
 ]
}