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 },
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 "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:\n",
      "TruSeq Adapter, Index 3 (100% over 50bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGC (1.02%)\n",
      "No Hit AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG (0.67%)\n",
      "TruSeq Adapter, Index 3 (100% over 50bp) ATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCC (0.47%)\n",
      "No Hit GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA (0.20%)\n",
      "\n",
      "F R2:\n",
      "Illumina Single End PCR Primer 1 (100% over 50bp) GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG (1.03%)\n",
      "No Hit TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC (0.31%)\n",
      "Illumina Single End PCR Primer 1 (100% over 50bp) ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT (0.28%)\n",
      "Illumina Single End PCR Primer 1 (98% over 50bp) ATCGGAAGAGCGTCGTGTAGGGAAAGAGGGTAGATCTCGGTGGTCGCCGT (0.12%)\n",
      "No Hit ACTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC (0.10%)\n",
      "\n",
      "T3D3 R1:\n",
      "TruSeq Adapter, Index 6 (100% over 50bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGC (1.97%)\n",
      "TruSeq Adapter, Index 6 (100% over 50bp) ATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCC (0.65%)\n",
      "\n",
      "T3D3 R2:\n",
      "Illumina Single End PCR Primer 1 (100% over 50bp) GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG (2.02%)\n",
      "Illumina Single End PCR Primer 1 (100% over 50bp) ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT (0.40%)\n",
      "Illumina Single End PCR Primer 1 (98% over 50bp) ATCGGAAGAGCGTCGTGTAGGGAAAGAGGGTAGATCTCGGTGGTCGCCGT (0.15%)\n",
      "\n",
      "T1D3 R1:\n",
      "TruSeq Adapter, Index 4 (100% over 50bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGC (1.48%)\n",
      "TruSeq Adapter, Index 4 (100% over 50bp) ATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGCC (0.23%)\n",
      "\n",
      "T1D3 R2:\n",
      "Illumina Single End PCR Primer 1 (100% over 50bp) GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG (1.51%)\n",
      "Illumina Single End PCR Primer 1 (100% over 50bp) ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT (0.15%)\n",
      "\n",
      "T1D5 R1:\n",
      "TruSeq Adapter, Index 5 (100% over 50bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGC (0.60%)\n",
      "TruSeq Adapter, Index 5 (100% over 50bp) ATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCC (0.25%)\n",
      "\n",
      "T1D5 R2:\n",
      "Illumina Single End PCR Primer 1 (100% over 50bp) GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG (0.62%)\n",
      "Illumina Single End PCR Primer 1 (100% over 50bp) ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT (0.17%)\n",
      "\n",
      "T3D5 R1:\n",
      "TruSeq Adapter, Index 7 (100% over 50bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGC (1.23%)\n",
      "TruSeq Adapter, Index 7 (100% over 50bp) ATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCC (0.19%)\n",
      "\n",
      "T3D5 R2:\n",
      "Illumina Single End PCR Primer 1 (100% over 50bp) GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG (1.28%)\n",
      "Illumina Single End PCR Primer 1 (100% over 50bp) ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT (0.19%)\n",
      "\n",
      "M1 R1:\n",
      "TruSeq Adapter, Index 8 (100% over 50bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGC (1.39%)\n",
      "TruSeq Adapter, Index 8 (100% over 50bp) ATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGCC (0.44%)\n",
      "\n",
      "M1 R2:\n",
      "Illumina Single End PCR Primer 1 (100% over 50bp) GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG (1.41%)\n",
      "Illumina Single End PCR Primer 1 (100% over 50bp) ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT (0.26%)\n",
      "Illumina Single End PCR Primer 1 (98% over 50bp) ATCGGAAGAGCGTCGTGTAGGGAAAGAGGGTAGATCTCGGTGGTCGCCGT (0.11%)\n",
      "\n",
      "M3 R1:\n",
      "TruSeq Adapter, Index 9 (100% over 50bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGATCTCGTATGC (0.75%)\n",
      "\n",
      "M3 R2:\n",
      "Illumina 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:\n",
      "No Hit AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG (1.00%)\n",
      "No Hit GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA (0.29%)\n",
      "TruSeq Adapter, Index 3 (100% over 50bp) ATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCC (0.21%)\n",
      "TruSeq Adapter, Index 3 (100% over 50bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGC (0.18%)\n",
      "No Hit TGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG (0.13%)\n",
      "\n",
      "F R2:\n",
      "No Hit TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC (0.36%)\n",
      "No Hit ACTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC (0.11%)\n",
      "\n",
      "T3D3 R1:\n",
      "TruSeq Adapter, Index 6 (100% over 50bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGC (0.73%)\n",
      "TruSeq Adapter, Index 6 (100% over 50bp) ATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCC (0.35%)\n",
      "\n",
      "T3D3 R2:\n",
      "No overrepresented sequences\n",
      "\n",
      "T1D3 R1:\n",
      "TruSeq Adapter, Index 4 (100% over 50bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGC (0.35%)\n",
      "\n",
      "T1D3 R2:\n",
      "No overrepresented sequences\n",
      "\n",
      "T1D5 R1:\n",
      "TruSeq Adapter, Index 5 (100% over 50bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGC (0.20%)\n",
      "TruSeq Adapter, Index 5 (100% over 50bp) ATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCC (0.13%)\n",
      "\n",
      "T1D5 R2:\n",
      "No overrepresented sequences\n",
      "\n",
      "T3D5 R1:\n",
      "TruSeq Adapter, Index 7 (100% over 50bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGC (0.52%)\n",
      "TruSeq Adapter, Index 7 (100% over 50bp) ATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCC (0.12%)\n",
      "\n",
      "T3D5 R2:\n",
      "No overrepresented sequences\n",
      "\n",
      "M1 R1:\n",
      "TruSeq Adapter, Index 8 (100% over 50bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGC (0.38%)\n",
      "TruSeq Adapter, Index 8 (100% over 50bp) ATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGCC (0.21%)\n",
      "\n",
      "M1 R2:\n",
      "No overrepresented sequences\n",
      "\n",
      "M3 R1:\n",
      "TruSeq Adapter, Index 9 (100% over 50bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGATCTCGTATGC (0.33%)\n",
      "\n",
      "M3 R2:\n",
      "No overrepresented sequences"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "#NOTEBOOK NAME\n",
      "nb='Larvae_Overrepresented_Sequences'\n",
      "\n",
      "#NOTEBOOK LOCATION\n",
      "nbloc='/Users/claireolson/Dropbox/Lab\\ \\(1\\)/IPython_nbs/Claire/'\n",
      "\n",
      "\n",
      "\n",
      "#TIMESTAMP\n",
      "date=!date +%m%d_%H%M\n",
      "#LOCATION OF POST DIRECTORY\n",
      "post='/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": {}
  }
 ]
}