{
 "metadata": {
  "name": "",
  "signature": "sha256:9cc23f775a6f26ff87bb606fd5db277288a5016d337db9d315b14de97a317dcd"
 },
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 "worksheets": [
  {
   "cells": [
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!/Applications/bioinfo/BSMAP/bsmap-2.74/samtools/samtools"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r\n",
        "Program: samtools (Tools for alignments in the SAM format)\r\n",
        "Version: 0.1.18 (r982:295)\r\n",
        "\r\n",
        "Usage:   samtools <command> [options]\r\n",
        "\r\n",
        "Command: view        SAM<->BAM conversion\r\n",
        "         sort        sort alignment file\r\n",
        "         mpileup     multi-way pileup\r\n",
        "         depth       compute the depth\r\n",
        "         faidx       index/extract FASTA\r\n",
        "         index       index alignment\r\n",
        "         idxstats    BAM index stats (r595 or later)\r\n",
        "         fixmate     fix mate information\r\n",
        "         flagstat    simple stats\r\n",
        "         calmd       recalculate MD/NM tags and '=' bases\r\n",
        "         merge       merge sorted alignments\r\n",
        "         rmdup       remove PCR duplicates\r\n",
        "         reheader    replace BAM header\r\n",
        "         cat         concatenate BAMs\r\n",
        "         targetcut   cut fosmid regions (for fosmid pool only)\r\n",
        "         phase       phase heterozygotes\r\n",
        "\r\n"
       ]
      }
     ],
     "prompt_number": 2
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "cd /Volumes/web/halfshell/qdod3/hs-rna/2M/"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "/Volumes/web/halfshell/qdod3/hs-rna/2M\n"
       ]
      }
     ],
     "prompt_number": 8
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!/Applications/bioinfo/BSMAP/bsmap-2.74/samtools/samtools \\\n",
      "sort \\\n",
      "/Volumes/web/halfshell/qdod3/hs-rna/2M/accepted_hits.bam \\\n",
      "sorted"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "[bam_sort_core] merging from 14 files...\r\n"
       ]
      }
     ],
     "prompt_number": 9
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!/Applications/bioinfo/BSMAP/bsmap-2.74/samtools/samtools \\\n",
      "index \\\n",
      "/Volumes/web/halfshell/qdod3/hs-rna/2M/accepted_hits.bam"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 11
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [],
     "language": "python",
     "metadata": {},
     "outputs": []
    }
   ],
   "metadata": {}
  }
 ]
}