{
 "metadata": {
  "name": ""
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [
    {
     "cell_type": "heading",
     "level": 4,
     "metadata": {},
     "source": [
      "Formatting files for methylKit using Giles code.  Below is the format from the methylKit manual of how files should be formatted to be read into the program."
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "<img src=\"http://eagle.fish.washington.edu/Mollusk/skitch/methylkit_-_R_package_for_DNA_methylation_analysis_-_Google_Project_Hosting_18F712DB.png\" alt=\"methylkit_-_R_package_for_DNA_methylation_analysis_-_Google_Project_Hosting_18F712DB.png\"/>"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!cd /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 12
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!chmod +x methratio.awk.sh"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "chmod: methratio.awk.sh: No such file or directory\r\n"
       ]
      }
     ],
     "prompt_number": 9
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!methratio.awk.sh /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methratio_out_CG5x_M1_tab.txt > /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methylKit_GilesCode/M1_methylkit.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "/bin/sh: methratio.awk.sh: command not found\r\n"
       ]
      }
     ],
     "prompt_number": 13
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [],
     "language": "python",
     "metadata": {},
     "outputs": []
    }
   ],
   "metadata": {}
  }
 ]
}