{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#Olympia Oyster transcriptome"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "See Geoduck page for details on how to download and check integretity of raw files.."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/Users/sr320/data-genomic/tentacle/OlyOv5\n"
     ]
    }
   ],
   "source": [
    "cd /Users/sr320/data-genomic/tentacle/OlyOv5"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/Users/sr320/data-genomic/tentacle/OlyOv5/PE\n"
     ]
    }
   ],
   "source": [
    "cd PE"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[31mfiltered_106A_Female_Mix_GATCAG_L004_R1.fastq\u001b[m\u001b[m*    \u001b[31mfiltered_108A_Female_Mix_GGCTAC_L004_R1.fastq\u001b[m\u001b[m*\r\n",
      "\u001b[31mfiltered_106A_Female_Mix_GATCAG_L004_R1.fastq.gz\u001b[m\u001b[m* \u001b[31mfiltered_108A_Female_Mix_GGCTAC_L004_R1.fastq.gz\u001b[m\u001b[m*\r\n",
      "\u001b[31mfiltered_106A_Female_Mix_GATCAG_L004_R2.fastq\u001b[m\u001b[m*    \u001b[31mfiltered_108A_Female_Mix_GGCTAC_L004_R2.fastq\u001b[m\u001b[m*\r\n",
      "\u001b[31mfiltered_106A_Female_Mix_GATCAG_L004_R2.fastq.gz\u001b[m\u001b[m* \u001b[31mfiltered_108A_Female_Mix_GGCTAC_L004_R2.fastq.gz\u001b[m\u001b[m*\r\n",
      "\u001b[31mfiltered_106A_Male_Mix_TAGCTT_L004_R1.fastq\u001b[m\u001b[m*      \u001b[31mfiltered_108A_Male_Mix_AGTCAA_L004_R1.fastq\u001b[m\u001b[m*\r\n",
      "\u001b[31mfiltered_106A_Male_Mix_TAGCTT_L004_R1.fastq.gz\u001b[m\u001b[m*   \u001b[31mfiltered_108A_Male_Mix_AGTCAA_L004_R1.fastq.gz\u001b[m\u001b[m*\r\n",
      "\u001b[31mfiltered_106A_Male_Mix_TAGCTT_L004_R2.fastq\u001b[m\u001b[m*      \u001b[31mfiltered_108A_Male_Mix_AGTCAA_L004_R2.fastq\u001b[m\u001b[m*\r\n",
      "\u001b[31mfiltered_106A_Male_Mix_TAGCTT_L004_R2.fastq.gz\u001b[m\u001b[m*   \u001b[31mfiltered_108A_Male_Mix_AGTCAA_L004_R2.fastq.gz\u001b[m\u001b[m*\r\n"
     ]
    }
   ],
   "source": [
    "ls"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "!cat \\\n",
    "filtered_106A_Female_Mix_GATCAG_L004_R1.fastq \\\n",
    "filtered_108A_Female_Mix_GGCTAC_L004_R1.fastq \\\n",
    "filtered_106A_Male_Mix_TAGCTT_L004_R1.fastq \\\n",
    "filtered_108A_Male_Mix_AGTCAA_L004_R1.fastq >> /Users/sr320/data-genomic/tentacle/OlyOv6/OlyOv6_combined_R1.fastq\n",
    "!cat \\\n",
    "filtered_106A_Female_Mix_GATCAG_L004_R2.fastq \\\n",
    "filtered_108A_Female_Mix_GGCTAC_L004_R2.fastq \\\n",
    "filtered_106A_Male_Mix_TAGCTT_L004_R2.fastq \\\n",
    "filtered_108A_Male_Mix_AGTCAA_L004_R2.fastq >> /Users/sr320/data-genomic/tentacle/OlyOv6/OlyOv6_combined_R2.fastq"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "!head R1.fastq\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "!/Applications/bioinfo/trim_galore_zip/trim_galore \\\n",
    "--paired \\\n",
    "--retain_unpaired \\\n",
    "--path_to_cutadapt /Users/sr320/.local/bin/cutadapt \\\n",
    "R1.fastq \\\n",
    "R2.fastq"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 2",
   "language": "python",
   "name": "python2"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 2
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython2",
   "version": "2.7.10"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 0
}