From 4e81fd840235ef7d654b4d9120d08abfb09f75f0 Mon Sep 17 00:00:00 2001
From: Julien Cornut <julien.cornut@hesge.ch>
Date: Fri, 26 Feb 2016 12:32:01 +0100
Subject: [PATCH] Automatic Update
---
ProcessFASTQ.ipynb | 32 +++++++++++++++++++++++++++++---
1 file changed, 29 insertions(+), 3 deletions(-)
diff --git a/ProcessFASTQ.ipynb b/ProcessFASTQ.ipynb
index 75e41e2..0ac866a 100644
--- a/ProcessFASTQ.ipynb
+++ b/ProcessFASTQ.ipynb
@@ -673,7 +673,7 @@
},
{
"cell_type": "code",
- "execution_count": 274,
+ "execution_count": 279,
"metadata": {
"collapsed": false
},
@@ -682,7 +682,26 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "28\tNM:i:0\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/testing.fastq 4-Bowtied/testing.sam\"\n",
+ "SN279:493:C84L3ACXX:4:2309:1272:2215\t4\t*\t0\t0\t*\t*\t0\t0\tNGAGGACCGAACCGACTTACGTT\t#1=DDFFFGGHHHIIJIJIJJFH\tXM:i:0\n",
+ "SN279:493:C84L3ACXX:4:2309:1275:2239\t4\t*\t0\t0\t*\t*\t0\t0\tTCAGGTTACCCGCGACAGGACGGAA\tCC@DFDEDHHDFHEEFIIIIGIE:@\tXM:i:0\n",
+ "SN279:493:C84L3ACXX:4:2309:2182:2231\t4\t*\t0\t0\t*\t*\t0\t0\tAAGATCCCTCGAAGATGACGAGGT\tCCCFFD>DDCDDFH@AFHIJIGE?\tXM:i:0\n",
+ "SN279:493:C84L3ACXX:4:2309:1652:2216\t0\tRDN25-1\t2545\t255\t24M\t*\t0\t0\tNCACGTTCTAGCATTCAAGGTCCC\t#1=BDDDDFFDBBGHGEEIEHIII\tXA:i:1\tMD:Z:0C23\tNM:i:1\n",
+ "SN279:493:C84L3ACXX:4:2309:2260:2244\t0\tRDN58-1\t131\t255\t28M\t*\t0\t0\tAGGGGGCATGCCTGTTTGAGCGTCATTT\tCCCFFFFFHHHHHIGIJJIJJJJJJIJJ\tXA:i:0\tMD:Z:28\tNM:i:0\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "@SN279:493:C84L3ACXX:4:2309:1272:2215 1:N:0:CAGATC\n",
+ "NGAGGACCGAACCGACTTACGTT\n",
+ "+\n",
+ "#1=DDFFFGGHHHIIJIJIJJFH\n",
+ "@SN279:493:C84L3ACXX:4:2309:1309:2236 1:N:0:CAGATC\n",
+ "CTTTCTTTACTTATTCAATGAAGCGGA\n",
+ "+\n",
+ "CCCFFDFFHHHHHJJJJJJJJJJJJJJ\n",
+ "@SN279:493:C84L3ACXX:4:2309:1275:2239 1:N:0:CAGATC\n",
+ "TCAGGTTACCCGCGACAGGACGGAA\n"
]
}
],
@@ -690,7 +709,14 @@
"%%bash \n",
"source ./source\n",
"\n",
- "sed -n 415,420p 4-Bowtied/$FILENAME.sam | hean"
+ "sed -n 415,420p 4-Bowtied/$FILENAME.sam\n",
+ "\n",
+ "echo\n",
+ "echo\n",
+ "echo\n",
+ "echo\n",
+ "\n",
+ "head 3-Filtered/$FILENAME.fastq"
]
},
{
--
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