From c89b1f122ec8b2170a48bda838f596a6e079e07d Mon Sep 17 00:00:00 2001
From: Julien Cornut <julien.cornut@hesge.ch>
Date: Thu, 25 Feb 2016 16:22:01 +0100
Subject: [PATCH] Automatic Update

---
 ProcessFASTQ.ipynb | 51 +++++++++++++++++++++++++++++++++++++++-------
 1 file changed, 44 insertions(+), 7 deletions(-)

diff --git a/ProcessFASTQ.ipynb b/ProcessFASTQ.ipynb
index 003a462..151ebb7 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",
-- 
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