{
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   "source": [
    "Giles did a reassembly on raw Oly ngs reads. \n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "![](http://eagle.fish.washington.edu/cnidarian/skitch/Transcriptome_assembly_methods_-_roberts_sbr_gmail_com_-_Gmail_1B3CA0E5.png)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "First step was cating\n",
    "\n",
    "```\n",
    "# Paired folder\n",
    "cat *_R2.fastq >> all.R2.fastq\n",
    "cat filtered_106A_Female_Mix_GATCAG_L004_R1.fastq \\\n",
    "    filtered_106A_Male_Mix_TAGCTT_L004_R1.fastq \\\n",
    "    filtered_108A_Female_Mix_GGCTAC_L004_R1.fastq >> all.R1.fastq\n",
    "\n",
    "# Unpaired folder\n",
    "cat *_R1.fastq >> tmp.R1.fastq\n",
    "\n",
    "# Then combining the two R1s\n",
    "cat tmp.R1.fastq >> all.R1.fastq\n",
    " \n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "---\n",
    "\n",
    "```\n",
    "\n",
    "#!/bin/bash\n",
    "\n",
    "export PATH=/share/bioinformatics/samtools-1.2:${PATH}\n",
    "export PATH=/share/bioinformatics/bowtie2:${PATH}\n",
    "export PATH=/share/bioinformatics/bowtie:${PATH}\n",
    "export TRIN=/share/bioinformatics/trinityrnaseq-2.0.6\n",
    "\n",
    "${TRIN}/Trinity \\\n",
    "    --seqType fq \\\n",
    "    --max_memory 44G \\\n",
    "    --left all.R1.fastq \\\n",
    "    --right all.R2.fastq \\\n",
    "    --CPU 6 \\\n",
    "    --normalize_reads\n",
    "```    "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Results"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "```\n",
    "\n",
    "################################\n",
    "## Counts of transcripts, etc.\n",
    "################################\n",
    "Total trinity 'genes':    129057\n",
    "Total trinity transcripts:    213990\n",
    "Percent GC: 39.07\n",
    "\n",
    "########################################\n",
    "Stats based on ALL transcript contigs:\n",
    "########################################\n",
    "\n",
    "    Contig N10: 5067\n",
    "    Contig N20: 3576\n",
    "    Contig N30: 2694\n",
    "    Contig N40: 2075\n",
    "    Contig N50: 1587\n",
    "\n",
    "    Median contig length: 446\n",
    "    Average contig: 886.10\n",
    "    Total assembled bases: 189616017\n",
    "\n",
    "\n",
    "#####################################################\n",
    "## Stats based on ONLY LONGEST ISOFORM per 'GENE':\n",
    "#####################################################\n",
    "\n",
    "    Contig N10: 4760\n",
    "    Contig N20: 3213\n",
    "    Contig N30: 2326\n",
    "    Contig N40: 1709\n",
    "    Contig N50: 1200\n",
    "\n",
    "    Median contig length: 372\n",
    "    Average contig: 722.55\n",
    "    Total assembled bases: 93250071\n",
    "        \n",
    "```        \n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      ">TR1|c0_g1_i1 len=489 path=[467:0-488] [-1, 467, -2]\r\n",
      "GTTTTGACCAACGAGAGTCGGTACTGAAGATGATCACTTGAAATAAAATTAAATGATAAC\r\n",
      "GTTTTCTTAAAACCCTTCATGTCGGCGTGATACATCCGTAGTTGAACGCCGTCACGAAAG\r\n",
      "GTAAGCCAAAGGGGGGTGTTGCAGTCCATACCCACACGTATAATTTATTCCATAAATAGT\r\n",
      "AGCAGCATAAAGCACACAATGATAATTTAAAATACGTTTCATTCACCAATGAATTAAGTA\r\n",
      "AGAATTGGTGCTTTTCCCTAGGTCTATTTGTCTGATCTTTTGTATGTCTGTTTATTGCTA\r\n",
      "AGTTGTTTGAGCCACCTCTTTTCCACACCTTATTTTGCTTACTCCTAGACACCTGATCCC\r\n",
      "AACTCTGCTATATCCACAGGTCCGTGCATGCGCTACACTTAATATTGTATTTCTATGGGA\r\n",
      "AACATTAGATAAATCACTGTTCATAAGAATAATGCTGTTTATATGTACAATGTACTTTCT\r\n",
      "TAATAAAAC\r\n",
      ">TR1|c1_g1_i1 len=430 path=[815:0-429] [-1, 815, -2]\r\n",
      "GGCAAACACAGATCCCTGGACGCACTACAGGTGGGATCAGGTGTCTAGGAGTAAGTAGCC\r\n",
      "CCTGTCGACAGGTTATATCCGCCGTGAGTCCCATATTTTGATCGGGTAAACGGAGCAATT\r\n",
      "GTGATAAAAATTAGTATATACATGTATAGAACGGTCTAACAATTGCAATGAAACCCGTCA\r\n",
      "GACAGCATTTGGTCCAATGGCGGGTTGTATTGGCAAACTAGATCTTTATAACGACCATAA\r\n",
      "CATTTCCGAAATGTGGATATTAACCGAAACTGTAGAAACCCCTGTAACACCACCTTGTTT\r\n",
      "GTCAGTAGCATGTCTCGACTTCAAACTAATCCTGCGCAGAACAAGCTCTTGCGTATTTAG\r\n",
      "TACGTTTAGAGACATACACACCTTATGCGGGTAATGATGGAATATTGCTGCATGGGGGTG\r\n",
      "GGAGGTTGAC\r\n",
      ">TR2|c0_g1_i1 len=254 path=[497:0-145 498:146-163 499:164-253] [-1, 497, 498, 499, -2]\r\n"
     ]
    }
   ],
   "source": [
    "!head -20 /Users/sr320/data-genomic/tentacle/OlyO-v4-transcriptome.fasta"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "213990\r\n"
     ]
    }
   ],
   "source": [
    "!fgrep -c \">\" /Users/sr320/data-genomic/tentacle/OlyO-v4-transcriptome.fasta"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
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