diff --git a/ProcessFASTQ.ipynb b/ProcessFASTQ.ipynb
index f4bb18109cab446be90f0a619ba51ffa3b4f7b2f..8286ad586fb1ca7766d9fe8e47fc0d77ed42b726 100644
--- a/ProcessFASTQ.ipynb
+++ b/ProcessFASTQ.ipynb
@@ -41,7 +41,7 @@
},
{
"cell_type": "code",
- "execution_count": 139,
+ "execution_count": 164,
"metadata": {
"collapsed": false
},
@@ -95,7 +95,7 @@
},
{
"cell_type": "code",
- "execution_count": 163,
+ "execution_count": 165,
"metadata": {
"collapsed": false
},
@@ -150,8 +150,8 @@
"# fname = \"flowcell384_lane7_pair1_ACAGTG\"\n",
"# fname = \"flowcell384_lane7_pair1_ACTTGA\"\n",
"# fname = \"flowcell384_lane7_pair1_CAGATC\"\n",
- "fname = \"flowcell384_lane7_pair1_GATCAG\"\n",
- "# fname = \"flowcell384_lane7_pair1_TGACCA\"\n",
+ "# fname = \"flowcell384_lane7_pair1_GATCAG\"\n",
+ "fname = \"flowcell384_lane7_pair1_TGACCA\"\n",
"\n",
"# Print available files in 0-Raws/ directory\n",
"\n",
@@ -208,7 +208,7 @@
},
{
"cell_type": "code",
- "execution_count": 141,
+ "execution_count": 166,
"metadata": {
"collapsed": false
},
@@ -231,7 +231,7 @@
},
{
"cell_type": "code",
- "execution_count": 142,
+ "execution_count": 167,
"metadata": {
"collapsed": false
},
@@ -239,10 +239,10 @@
{
"data": {
"text/plain": [
- "'flowcell384_lane7_pair1_GATCAG.fastq.gz'"
+ "'flowcell384_lane7_pair1_TGACCA.fastq.gz'"
]
},
- "execution_count": 142,
+ "execution_count": 167,
"metadata": {},
"output_type": "execute_result"
}
@@ -266,7 +266,7 @@
},
{
"cell_type": "code",
- "execution_count": 143,
+ "execution_count": 168,
"metadata": {
"collapsed": false
},
@@ -276,12 +276,12 @@
"output_type": "stream",
"text": [
"\n",
- "flowcell384_lane7_pair1_GATCAG\n",
+ "flowcell384_lane7_pair1_TGACCA\n",
"\n",
- "@SN279:498:C88PKACXX:7:1109:1982:2231 1:N:0:GATCAG\n",
- "NATAGTGTAGTGGTTATCACTTTCGCTGTAGGCACCATCAATAGATCGGAA\n",
+ "@SN279:498:C88PKACXX:7:1109:1699:2220 1:N:0:TGACCA\n",
+ "NGAGGTGCACAATCGACCGATCCTGCTGTAGGCACCATCAATAGATCGGAA\n",
"+\n",
- "#1:DDFFFHFCFHCGIIJJJJJJAHHIJJIIIJJIJIJIIGIGIJJIJJII\n"
+ "#1=D;DDDHHFHHIIIIIIIIIIIIIIIIHIIIIFHIIIIIHHIIIIIIII\n"
]
}
],
@@ -303,7 +303,7 @@
},
{
"cell_type": "code",
- "execution_count": 144,
+ "execution_count": 169,
"metadata": {
"collapsed": false
},
@@ -312,7 +312,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "Processing will take approximatively 0 hour(s) 30 minute(s) and 43 second(s)\n"
+ "Processing will take approximatively 0 hour(s) 44 minute(s) and 38 second(s)\n"
]
}
],
@@ -358,7 +358,7 @@
},
{
"cell_type": "code",
- "execution_count": 145,
+ "execution_count": null,
"metadata": {
"collapsed": false
},
@@ -370,21 +370,11 @@
},
{
"cell_type": "code",
- "execution_count": 146,
+ "execution_count": null,
"metadata": {
"collapsed": false
},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "This is cutadapt 1.9.1 with Python 3.5.1\n",
- "Command line parameters: -a CTGTAGGCACCATCAATAGATCGGAA -o 1-Cutadapted/flowcell384_lane7_pair1_GATCAG.fastq.gz --quiet flowcell384_lane7_pair1_GATCAG.fastq.gz\n",
- "Trimming 1 adapter with at most 10.0% errors in single-end mode ...\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"%%bash\n",
"source ./source\n",
@@ -402,19 +392,11 @@
},
{
"cell_type": "code",
- "execution_count": 147,
+ "execution_count": null,
"metadata": {
"collapsed": false
},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Cutadapt run time : 0:27:05.246443\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"# Store current time\n",
"after = datetime.datetime.now()\n",
@@ -427,7 +409,7 @@
},
{
"cell_type": "code",
- "execution_count": 148,
+ "execution_count": null,
"metadata": {
"collapsed": true
},
@@ -448,7 +430,7 @@
},
{
"cell_type": "code",
- "execution_count": 149,
+ "execution_count": null,
"metadata": {
"collapsed": false
},
@@ -460,7 +442,7 @@
},
{
"cell_type": "code",
- "execution_count": 150,
+ "execution_count": null,
"metadata": {
"collapsed": false
},
@@ -475,19 +457,11 @@
},
{
"cell_type": "code",
- "execution_count": 151,
+ "execution_count": null,
"metadata": {
"collapsed": false
},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Zcat run time : 0:00:27.042865\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"# Store current time\n",
"after = datetime.datetime.now()\n",
@@ -513,7 +487,7 @@
},
{
"cell_type": "code",
- "execution_count": 152,
+ "execution_count": null,
"metadata": {
"collapsed": false
},
@@ -525,7 +499,7 @@
},
{
"cell_type": "code",
- "execution_count": 153,
+ "execution_count": null,
"metadata": {
"collapsed": true
},
@@ -550,19 +524,11 @@
},
{
"cell_type": "code",
- "execution_count": 154,
+ "execution_count": null,
"metadata": {
"collapsed": false
},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Filtering run time : 0:24:28.649445\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"# Store current time\n",
"after = datetime.datetime.now()\n",
@@ -598,28 +564,12 @@
},
{
"cell_type": "code",
- "execution_count": 155,
+ "execution_count": null,
"metadata": {
"collapsed": false,
"scrolled": false
},
- "outputs": [
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "Time loading forward index: 00:00:00\n",
- "Time loading mirror index: 00:00:01\n",
- "End-to-end 2/3-mismatch full-index search: 00:02:56\n",
- "# reads processed: 32558526\n",
- "# reads with at least one reported alignment: 24915112 (76.52%)\n",
- "# reads that failed to align: 7643414 (23.48%)\n",
- "Reported 24915112 alignments to 1 output stream(s)\n",
- "Time searching: 00:02:57\n",
- "Overall time: 00:02:57\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"%%bash\n",
"source ./source\n",
@@ -668,7 +618,7 @@
},
{
"cell_type": "code",
- "execution_count": 156,
+ "execution_count": null,
"metadata": {
"collapsed": false
},
@@ -681,24 +631,11 @@
},
{
"cell_type": "code",
- "execution_count": 157,
+ "execution_count": null,
"metadata": {
"collapsed": false
},
- "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"
- ]
- }
- ],
+ "outputs": [],
"source": [
"with open(\"3-Filtered/\" +fname+\".fastq\",\"r\") as filtered, \\\n",
" open(\"4-Bowtied/\" +fname+\".sam\",\"r\") as matches, \\\n",
@@ -726,19 +663,11 @@
},
{
"cell_type": "code",
- "execution_count": 158,
+ "execution_count": null,
"metadata": {
"collapsed": false
},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Filtering non-codant tRNA run time : 0:17:11.459755\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"# Store current time\n",
"after = datetime.datetime.now()\n",
@@ -760,27 +689,11 @@
},
{
"cell_type": "code",
- "execution_count": 159,
+ "execution_count": null,
"metadata": {
"collapsed": false
},
- "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"
- ]
- }
- ],
+ "outputs": [],
"source": [
"%%bash\n",
"source ./source\n",
@@ -805,7 +718,7 @@
},
{
"cell_type": "code",
- "execution_count": 160,
+ "execution_count": null,
"metadata": {
"collapsed": true
},
@@ -836,7 +749,7 @@
},
{
"cell_type": "code",
- "execution_count": 161,
+ "execution_count": null,
"metadata": {
"collapsed": false
},
@@ -880,7 +793,7 @@
},
{
"cell_type": "code",
- "execution_count": 162,
+ "execution_count": null,
"metadata": {
"collapsed": false
},