diff --git a/ProcessFASTQ.ipynb b/ProcessFASTQ.ipynb index 1ba5cb8530bdad1f51c38061d095120b6f6ffaa4..1436522ac5523ca227572e6807710f388f0f5ed6 100644 --- a/ProcessFASTQ.ipynb +++ b/ProcessFASTQ.ipynb @@ -95,7 +95,7 @@ }, { "cell_type": "code", - "execution_count": 191, + "execution_count": 214, "metadata": { "collapsed": false }, @@ -114,7 +114,7 @@ "flowcell362_lane4_pair1_ACTTGA \t\t Processsed\n", "flowcell362_lane4_pair1_CAGATC \t\t Processsed\n", "flowcell362_lane4_pair1_TGACCA \t\t Processsed\n", - "flowcell362_lane4_pair1_Undetermined\n", + "flowcell362_lane4_pair1_Undetermined \t\t Processsed\n", "flowcell384_lane7_pair1_ACAGTG \t\t Processsed\n", "flowcell384_lane7_pair1_ACTTGA \t\t Processsed\n", "flowcell384_lane7_pair1_CAGATC \t\t Processsed\n", @@ -726,7 +726,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 209, "metadata": { "collapsed": false }, @@ -760,11 +760,27 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 210, "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: 00:00:30\n", + "# reads processed: 2599991\n", + "# reads with at least one reported alignment: 439705 (16.91%)\n", + "# reads that failed to align: 2160286 (83.09%)\n", + "Reported 439705 alignments to 1 output stream(s)\n", + "Time searching: 00:00:30\n", + "Overall time: 00:00:30\n" + ] + } + ], "source": [ "%%bash\n", "source ./source\n", @@ -789,7 +805,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 211, "metadata": { "collapsed": true }, @@ -820,7 +836,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 212, "metadata": { "collapsed": false }, @@ -864,7 +880,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 213, "metadata": { "collapsed": false },