diff --git a/ProcessFASTQ.ipynb b/ProcessFASTQ.ipynb index 003a462f121d9795b703080c5a9cfd0c2fcea5d6..151ebb77c0646bb50b7bfa4e72884811e43d0603 100644 --- a/ProcessFASTQ.ipynb +++ b/ProcessFASTQ.ipynb @@ -668,7 +668,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 156, "metadata": { "collapsed": false }, @@ -681,11 +681,24 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 157, "metadata": { "collapsed": false }, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "@SQ\tSN:tW(UCA)Q\tLN:74\n", + "\n", + "@SQ\tSN:tY(GUA)Q\tLN:84\n", + "\n", + "@PG\tID:Bowtie\tVN:1.1.2\tCL:\"bowtie --wrapper basic-0 -S -v 3 -p 8 --time --best ref/2-Indexes/Yeast-Noncoding/Yeast-Noncoding 3-Filtered/flowcell384_lane7_pair1_GATCAG.fastq 4-Bowtied/flowcell384_lane7_pair1_GATCAG.sam\"\n", + "\n" + ] + } + ], "source": [ "with open(\"3-Filtered/\" +fname+\".fastq\",\"r\") as filtered, \\\n", " open(\"4-Bowtied/\" +fname+\".sam\",\"r\") as matches, \\\n", @@ -713,11 +726,19 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 158, "metadata": { "collapsed": false }, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Filtering non-codant tRNA run time : 0:17:11.459755\n" + ] + } + ], "source": [ "# Store current time\n", "after = datetime.datetime.now()\n", @@ -739,11 +760,27 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 159, "metadata": { "collapsed": false }, - "outputs": [], + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Time loading forward index: 00:00:00\n", + "Time loading mirror index: 00:00:00\n", + "End-to-end 2/3-mismatch full-index search: 00:00:40\n", + "# reads processed: 7643414\n", + "# reads with at least one reported alignment: 6626979 (86.70%)\n", + "# reads that failed to align: 1016435 (13.30%)\n", + "Reported 6626979 alignments to 1 output stream(s)\n", + "Time searching: 00:00:40\n", + "Overall time: 00:00:40\n" + ] + } + ], "source": [ "%%bash\n", "source ./source\n",