From 690c44cf4bbad9b8c5d1afa43507d24931247fae Mon Sep 17 00:00:00 2001
From: Julien Cornut <julien.cornut@hesge.ch>
Date: Fri, 26 Feb 2016 11:24:01 +0100
Subject: [PATCH] Automatic Update
---
ProcessFASTQ.ipynb | 106 +++++++++++++++++++++++----------------------
1 file changed, 54 insertions(+), 52 deletions(-)
diff --git a/ProcessFASTQ.ipynb b/ProcessFASTQ.ipynb
index 1436522..3555de0 100644
--- a/ProcessFASTQ.ipynb
+++ b/ProcessFASTQ.ipynb
@@ -41,7 +41,7 @@
},
{
"cell_type": "code",
- "execution_count": 190,
+ "execution_count": 215,
"metadata": {
"collapsed": false
},
@@ -95,7 +95,7 @@
},
{
"cell_type": "code",
- "execution_count": 214,
+ "execution_count": 216,
"metadata": {
"collapsed": false
},
@@ -139,6 +139,8 @@
"\n",
"# Enter/Uncomment here the name of the file you want to process\n",
"\n",
+ "fname = \"testing\"\n",
+ "\n",
"# fname = \"Undetermined_lane7_pair1\"\n",
"# fname = \"flowcell261_lane8_pair1_CAGATC\"\n",
"# fname = \"flowcell261_lane8_pair1_TGACCA\"\n",
@@ -146,7 +148,7 @@
"# fname = \"flowcell362_lane4_pair1_ACTTGA\"\n",
"# fname = \"flowcell362_lane4_pair1_CAGATC\"\n",
"# fname = \"flowcell362_lane4_pair1_TGACCA\"\n",
- "fname = \"flowcell362_lane4_pair1_Undetermined\"\n",
+ "# fname = \"flowcell362_lane4_pair1_Undetermined\"\n",
"# fname = \"flowcell384_lane7_pair1_ACAGTG\"\n",
"# fname = \"flowcell384_lane7_pair1_ACTTGA\"\n",
"# fname = \"flowcell384_lane7_pair1_CAGATC\"\n",
@@ -208,7 +210,7 @@
},
{
"cell_type": "code",
- "execution_count": 192,
+ "execution_count": 217,
"metadata": {
"collapsed": false
},
@@ -231,7 +233,7 @@
},
{
"cell_type": "code",
- "execution_count": 193,
+ "execution_count": 218,
"metadata": {
"collapsed": false
},
@@ -239,10 +241,10 @@
{
"data": {
"text/plain": [
- "'flowcell362_lane4_pair1_Undetermined.fastq.gz'"
+ "'testing.fastq.gz'"
]
},
- "execution_count": 193,
+ "execution_count": 218,
"metadata": {},
"output_type": "execute_result"
}
@@ -266,7 +268,7 @@
},
{
"cell_type": "code",
- "execution_count": 194,
+ "execution_count": 219,
"metadata": {
"collapsed": false
},
@@ -276,12 +278,12 @@
"output_type": "stream",
"text": [
"\n",
- "flowcell362_lane4_pair1_Undetermined\n",
+ "testing\n",
"\n",
- "@SN279:493:C84L3ACXX:4:2309:1848:2226 1:N:0:TTCCGT\n",
- "NCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTC\n",
+ "@SN279:493:C84L3ACXX:4:2309:1272:2215 1:N:0:CAGATC\n",
+ "NGAGGACCGAACCGACTTACGTTCTGTAGGCACCATCAATAGATCGGAAGA\n",
"+\n",
- "#4=DDDDDHHHHHIHFHJJJJJJJJIJJJHIJJJJJJJJJJJJJJJIJJJJ\n"
+ "#1=DDFFFGGHHHIIJIJIJJFHGHIFGHIGIJIJIGIHJGGHIHIJJIEE\n"
]
}
],
@@ -303,7 +305,7 @@
},
{
"cell_type": "code",
- "execution_count": 195,
+ "execution_count": 220,
"metadata": {
"collapsed": false
},
@@ -312,7 +314,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "Processing will take approximatively 0 hour(s) 3 minute(s) and 31 second(s)\n"
+ "Processing will take approximatively 0 hour(s) 0 minute(s) and 0 second(s)\n"
]
}
],
@@ -358,7 +360,7 @@
},
{
"cell_type": "code",
- "execution_count": 196,
+ "execution_count": 221,
"metadata": {
"collapsed": false
},
@@ -370,7 +372,7 @@
},
{
"cell_type": "code",
- "execution_count": 197,
+ "execution_count": 222,
"metadata": {
"collapsed": false
},
@@ -380,7 +382,7 @@
"output_type": "stream",
"text": [
"This is cutadapt 1.9.1 with Python 3.5.1\n",
- "Command line parameters: -a CTGTAGGCACCATCAATAGATCGGAA -o 1-Cutadapted/flowcell362_lane4_pair1_Undetermined.fastq.gz --quiet flowcell362_lane4_pair1_Undetermined.fastq.gz\n",
+ "Command line parameters: -a CTGTAGGCACCATCAATAGATCGGAA -o 1-Cutadapted/testing.fastq.gz --quiet testing.fastq.gz\n",
"Trimming 1 adapter with at most 10.0% errors in single-end mode ...\n"
]
}
@@ -402,7 +404,7 @@
},
{
"cell_type": "code",
- "execution_count": 198,
+ "execution_count": 223,
"metadata": {
"collapsed": false
},
@@ -411,7 +413,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "Cutadapt run time : 0:03:24.043250\n"
+ "Cutadapt run time : 0:00:00.282434\n"
]
}
],
@@ -427,7 +429,7 @@
},
{
"cell_type": "code",
- "execution_count": 199,
+ "execution_count": 224,
"metadata": {
"collapsed": true
},
@@ -448,7 +450,7 @@
},
{
"cell_type": "code",
- "execution_count": 200,
+ "execution_count": 225,
"metadata": {
"collapsed": false
},
@@ -460,7 +462,7 @@
},
{
"cell_type": "code",
- "execution_count": 201,
+ "execution_count": 226,
"metadata": {
"collapsed": false
},
@@ -475,7 +477,7 @@
},
{
"cell_type": "code",
- "execution_count": 202,
+ "execution_count": 227,
"metadata": {
"collapsed": false
},
@@ -484,7 +486,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "Zcat run time : 0:00:03.973413\n"
+ "Zcat run time : 0:00:00.258304\n"
]
}
],
@@ -513,7 +515,7 @@
},
{
"cell_type": "code",
- "execution_count": 203,
+ "execution_count": 228,
"metadata": {
"collapsed": false
},
@@ -525,7 +527,7 @@
},
{
"cell_type": "code",
- "execution_count": 204,
+ "execution_count": 229,
"metadata": {
"collapsed": true
},
@@ -550,7 +552,7 @@
},
{
"cell_type": "code",
- "execution_count": 205,
+ "execution_count": 230,
"metadata": {
"collapsed": false
},
@@ -559,7 +561,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "Filtering run time : 0:02:37.166601\n"
+ "Filtering run time : 0:00:00.337490\n"
]
}
],
@@ -598,7 +600,7 @@
},
{
"cell_type": "code",
- "execution_count": 206,
+ "execution_count": 231,
"metadata": {
"collapsed": false,
"scrolled": false
@@ -610,13 +612,13 @@
"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: 00:00:34\n",
- "# reads processed: 3112673\n",
- "# reads with at least one reported alignment: 512682 (16.47%)\n",
- "# reads that failed to align: 2599991 (83.53%)\n",
- "Reported 512682 alignments to 1 output stream(s)\n",
- "Time searching: 00:00:34\n",
- "Overall time: 00:00:34\n"
+ "End-to-end 2/3-mismatch full-index search: 00:00:00\n",
+ "# reads processed: 1000\n",
+ "# reads with at least one reported alignment: 555 (55.50%)\n",
+ "# reads that failed to align: 445 (44.50%)\n",
+ "Reported 555 alignments to 1 output stream(s)\n",
+ "Time searching: 00:00:00\n",
+ "Overall time: 00:00:00\n"
]
}
],
@@ -668,7 +670,7 @@
},
{
"cell_type": "code",
- "execution_count": 207,
+ "execution_count": 232,
"metadata": {
"collapsed": false
},
@@ -681,7 +683,7 @@
},
{
"cell_type": "code",
- "execution_count": 208,
+ "execution_count": 233,
"metadata": {
"collapsed": false
},
@@ -694,7 +696,7 @@
"\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/flowcell362_lane4_pair1_Undetermined.fastq 4-Bowtied/flowcell362_lane4_pair1_Undetermined.sam\"\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",
"\n"
]
}
@@ -726,7 +728,7 @@
},
{
"cell_type": "code",
- "execution_count": 209,
+ "execution_count": 234,
"metadata": {
"collapsed": false
},
@@ -735,7 +737,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "Filtering non-codant tRNA run time : 0:02:31.047781\n"
+ "Filtering non-codant tRNA run time : 0:00:01.407564\n"
]
}
],
@@ -760,7 +762,7 @@
},
{
"cell_type": "code",
- "execution_count": 210,
+ "execution_count": 235,
"metadata": {
"collapsed": false
},
@@ -771,13 +773,13 @@
"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"
+ "End-to-end 2/3-mismatch full-index search: 00:00:00\n",
+ "# reads processed: 445\n",
+ "# reads with at least one reported alignment: 240 (53.93%)\n",
+ "# reads that failed to align: 205 (46.07%)\n",
+ "Reported 240 alignments to 1 output stream(s)\n",
+ "Time searching: 00:00:00\n",
+ "Overall time: 00:00:00\n"
]
}
],
@@ -805,7 +807,7 @@
},
{
"cell_type": "code",
- "execution_count": 211,
+ "execution_count": 236,
"metadata": {
"collapsed": true
},
@@ -836,7 +838,7 @@
},
{
"cell_type": "code",
- "execution_count": 212,
+ "execution_count": 237,
"metadata": {
"collapsed": false
},
@@ -880,7 +882,7 @@
},
{
"cell_type": "code",
- "execution_count": 213,
+ "execution_count": 238,
"metadata": {
"collapsed": false
},
--
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