{
 "metadata": {
  "name": ""
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [
    {
     "cell_type": "heading",
     "level": 1,
     "metadata": {},
     "source": [
      "Larvae Example Workflow- M1 Data (Spermatozoa from Male 1)"
     ]
    },
    {
     "cell_type": "heading",
     "level": 2,
     "metadata": {},
     "source": [
      "This is an example of my workflow for my bisulfite sequencing larvae dataset.  I am working with a total of 28 files and will narrow it down to a workflow of 7 datasets (1 female/eggs, 2 males/sperm, and 4 larvae samples)"
     ]
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": [
      "1. Upload raw data to iPlant and unzip/uncompress this file this file using the gunzip analysis application"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "<img src=\"http://eagle.fish.washington.edu/Mollusk/skitch/_87__Discovery_Environment_18C6A781.png\" alt=\"_87__Discovery_Environment_18C6A781.png\"/>"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "<img src=\"http://eagle.fish.washington.edu/Mollusk/skitch/_87__Discovery_Environment_18C6A7B0.png\" alt=\"_87__Discovery_Environment_18C6A7B0.png\"/>"
     ]
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": [
      "2. Dowload uncompressed files and relocate to Eagle"
     ]
    },
    {
     "cell_type": "heading",
     "level": 4,
     "metadata": {},
     "source": [
      "File locations for M1 uncompressed (Nov): http://eagle.fish.washington.edu/Mollusk/index.php?dir=bs_larvae_exp%2FUncompressed_Nov%2F"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "<img src=\"http://eagle.fish.washington.edu/Mollusk/skitch/Directory_Listing_of__Mollusk_bs_larvae_exp_Uncompressed_Nov_18C6A8BC.png\" alt=\"Directory_Listing_of__Mollusk_bs_larvae_exp_Uncompressed_Nov_18C6A8BC.png\"/>"
     ]
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": [
      "3. Concatenate November and September uncompressed files (R1 and R2 separate).  These are technical replicates from the Bisulfite sequencing run."
     ]
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": [
      "M1_R1"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgM1_ACTTGA_L004_R1.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgM1_ACTTGA_L007_R1.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M1_R1.fastq"
     ],
     "language": "python",
     "metadata": {},
     "outputs": []
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": [
      "M1_R2"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgM1_ACTTGA_L004_R2.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgM1_ACTTGA_L007_R2.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M1_R2.fastq "
     ],
     "language": "python",
     "metadata": {},
     "outputs": []
    },
    {
     "cell_type": "heading",
     "level": 4,
     "metadata": {},
     "source": [
      "Location of concatenated files:"
     ]
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": [
      "R1: http://eagle.fish.washington.edu/Mollusk/index.php?dir=bs_larvae_exp%2FConcatenated_Files_R1%2F"
     ]
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": [
      "R2: http://eagle.fish.washington.edu/Mollusk/index.php?dir=bs_larvae_exp%2FConcatenated_Files_R2%2F"
     ]
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": [
      "4. Upload these files to iPlant using the \"Import from URL\" function.  This allows me to import multiple files from the URL location on Eagle.  "
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "<img src=\"http://eagle.fish.washington.edu/Mollusk/skitch/_87__Discovery_Environment_18C6AB07.png\" alt=\"_87__Discovery_Environment_18C6AB07.png\"/>"
     ]
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": [
      "5. Run BSMAP in iPlant"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "<img src=\"http://eagle.fish.washington.edu/Mollusk/skitch/_87__Discovery_Environment_18C6AD33.png\" alt=\"_87__Discovery_Environment_18C6AD33.png\"/>"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "<img src=\"http://eagle.fish.washington.edu/Mollusk/skitch/_87__Discovery_Environment_18C6AD66.png\" alt=\"_87__Discovery_Environment_18C6AD66.png\"/>"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "<img src=\"http://eagle.fish.washington.edu/Mollusk/skitch/_87__Discovery_Environment_18C6AD66.png\" alt=\"_87__Discovery_Environment_18C6AD66.png\"/>"
     ]
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": [
      "6. Download files frim iPlant and run methratio in iPython"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [],
     "language": "python",
     "metadata": {},
     "outputs": []
    }
   ],
   "metadata": {}
  }
 ]
}