Dinh/Dinh 2015/NOTES/2015-1-7
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141216_HiSeqRapidRun
- Processed files are copied to genome-miner at: /media/Ext12T/DD_Ext12T/MONOD/141216_HiSeqRapidRunWGBS
- Sub-directories: BAMfiles, MethylFreq, BEDfiles
- Library information from Noi: http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-12-25
- Perform trimming with trim-galore and mapping with bwa mem
- For trimming, use methylated adaptors sequences, quality trim with -q 20 from 3' ends, and trim 5 bp from 5' ends (methylation bias)
- Use tscc with 4 processors per node
Mapping steps
- Make a table:
PC-P_2 /oasis/tscc/scratch/ddiep/Working/150106_HiSeqRapidWGBS/Fastq s_1_1_ILMN_Indx01.txt,s_1_2_ILMN_Indx01.txt 64 none AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT WGBS PC-P_4 /oasis/tscc/scratch/ddiep/Working/150106_HiSeqRapidWGBS/Fastq s_1_1_ILMN_Indx03.txt,s_1_2_ILMN_Indx03.txt 64 none AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT WGBS NC-7 /oasis/tscc/scratch/ddiep/Working/150106_HiSeqRapidWGBS/Fastq s_1_1_ILMN_Indx07.txt,s_1_2_ILMN_Indx07.txt 64 none AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT WGBS PC-P_9 /oasis/tscc/scratch/ddiep/Working/150106_HiSeqRapidWGBS/Fastq s_1_1_ILMN_Indx08.txt,s_1_2_ILMN_Indx08.txt 64 none AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT WGBS 6-P-1 /oasis/tscc/scratch/ddiep/Working/150106_HiSeqRapidWGBS/Fastq s_1_1_ILMN_Indx09.txt,s_1_2_ILMN_Indx09.txt 64 none AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT WGBS ...
- Split table file into 27 files, 1 line/sample per file:
split -l 1 list_my_files aa_
- Run Go.Map.sh script on tscc, each sample will be processed on a separate node.
#===Change the following paths===# cur_dir=`pwd` scripts_dir="/home/ddiep/scripts/BisReadMapper/src" #===Begin===# for n in aa_aa aa_ap aa_ab aa_ac aa_ad aa_ae aa_af aa_ag aa_ah aa_ai aa_aj aa_ak aa_al aa_am aa_an aa_ao aa_aq aa_ar aa_as aa_at aa_au aa_av aa_aw aa_ax aa_ay aa_az aa_ba do #1) Run mapper: echo "#!/bin/csh" > $n.job echo "#PBS -l nodes=1:ppn=4" >> $n.job echo "#PBS -l walltime=14:00:00" >> $n.job echo "#PBS -o $n.log" >> $n.job echo "#PBS -e $n.err" >> $n.job echo "#PBS -V" >> $n.job echo "#PBS -M diep.hue.dinh@gmail.com" >> $n.job echo "#PBS -m abe" >> $n.job echo "#PBS -A k4zhang-group" >> $n.job echo "cd /state/partition1/\$USER/\$PBS_JOBID" >> $n.job #echo "cd $cur_dir" >> $n.job echo "$scripts_dir/MasterBisReadMapper.pl -i $cur_dir/$n -s $cur_dir/list_paths_Hg19 -b yes > $cur_dir/$n.status" >> $n.job echo "cp -r * $cur_dir/" >> $n.job qsub -q hotel $n.job done #===End===#
Mapping statistics
SAMPLE ID | Total PE reads | Total reads | Total reads after trimming | Total mapped reads | %trimmed | %mapped |
6-P-1_map | 6,304,203 | 12,608,406 | 11,953,618 | 10,355,738 | 5% | 87% |
6-P-2_map | 6,984,763 | 13,969,526 | 13,303,090 | 11,570,287 | 5% | 87% |
6-P-3_map | 7,758,987 | 15,517,974 | 14,491,124 | 12,482,525 | 7% | 86% |
6T-1_map | 7,086,511 | 14,173,022 | 13,834,798 | 11,869,709 | 2% | 86% |
6T-2_map | 7,489,616 | 14,979,232 | 14,638,550 | 12,820,323 | 2% | 88% |
6T-3_map | 23,044,384 | 46,088,768 | 45,125,296 | 36,126,640 | 2% | 80% |
6T-4_map | 7,345,257 | 14,690,514 | 14,302,984 | 12,351,984 | 3% | 86% |
6T-5_map | 8,242,846 | 16,485,692 | 16,084,486 | 13,871,915 | 2% | 86% |
7-P-10_map | 6,405,081 | 12,810,162 | 12,126,962 | 10,375,497 | 5% | 86% |
7-P-3_map | 5,117,607 | 10,235,214 | 9,714,174 | 8,343,291 | 5% | 86% |
7-P-5_map | 5,943,036 | 11,886,072 | 11,311,240 | 9,868,792 | 5% | 87% |
7-P-6_map | 8,151,067 | 16,302,134 | 15,454,040 | 13,420,765 | 5% | 87% |
7-P-7_map | 8,006,228 | 16,012,456 | 15,215,062 | 13,264,972 | 5% | 87% |
7-P-8_map | 6,321,921 | 12,643,842 | 11,948,422 | 10,309,480 | 6% | 86% |
7T-1_map | 7,397,882 | 14,795,764 | 14,414,610 | 12,579,473 | 3% | 87% |
7T-2_map | 7,913,136 | 15,826,272 | 15,471,842 | 13,386,508 | 2% | 87% |
7T-4_map | 7,428,250 | 14,856,500 | 14,495,860 | 12,632,367 | 2% | 87% |
7T-5_map | 7,933,340 | 15,866,680 | 15,474,202 | 13,465,056 | 2% | 87% |
NC-7_map | 8,140,557 | 16,281,114 | 15,329,258 | 11,685,910 | 6% | 76% |
PC-P_2_map | 6,236,300 | 12,472,600 | 11,848,168 | 10,306,946 | 5% | 87% |
PC-P_4_map | 6,400,370 | 12,800,740 | 12,191,246 | 10,561,291 | 5% | 87% |
PC-P_9_map | 7,500,258 | 15,000,516 | 14,213,460 | 12,272,000 | 5% | 86% |
PCT-1_map | 7,092,180 | 14,184,360 | 13,848,186 | 11,921,316 | 2% | 86% |
PCT-2_map | 8,566,243 | 17,132,486 | 16,739,144 | 14,465,075 | 2% | 86% |
PCT-4_map | 8,189,668 | 16,379,336 | 16,003,166 | 13,781,204 | 2% | 86% |
PCT-6_map | 9,228,450 | 18,456,900 | 17,987,752 | 15,681,405 | 3% | 87% |
PCT-7_map | 7,697,260 | 15,394,520 | 15,030,202 | 12,980,554 | 2% | 86% |