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 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Quality Control\n",
    "<!--\n",
    "** Add Intro Text***\n",
    "-->\n",
    "\n",
    "## Shell Variables\n",
    "Assign the variables in this notebook."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "# We used these in the last notebook\n",
    "CUROUT=$HOME/work/scratch/2015_output\n",
    "DEMUX=$CUROUT/demux_fastqs\n",
    "\n",
    "# The following are new for this notebook\n",
    "QC=$CUROUT/qc_output"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Making New Directories\n",
    "The directories *do* carry over between notebooks, they are a function of the server, so we only need to make the directories that are new in this notebook"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "mkdir -p $QC"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Now let's check to be sure that worked.  We will run `ls` and check that these directories now exist in the `$OUTPUT` directory."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "ls $CUROUT"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Fastqc\n",
    "Now that we have had a quick look at our fastq file, let's run some basic analysis using a program called fastqc.  This will take less than a minute to run.  Remember that while \"long\" jobs are running it will say \"In [\\*]:\" in the left margin, once it is done, a number will replace the asterisk."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "fastqc -h"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "# fastqc --threads 2 --quiet $DEMUX/r1.8A_pilot.fq.gz -o $QC\n",
    "fastqc $DEMUX/r1.8A_pilot.fq.gz -o $QC"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Once fastqc is done running you can click here to view the [fastqc report](/files/scratch/2015_output/qc_output/r1.8A_pilot.fq_fastqc.html)"
   ]
  }
 ],
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