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* [[http://genome-tech.ucsd.edu/LabNotes/index.php/noi:DMR220k_LabNotes '''Link to calendar''']] = Mapping of ASM and ASCM samples in human cells project to hg19 = * Capture experiment on: http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-5-24, http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-5-31 * The libraries were sequenced on HiSeq 120608_SN1001 run (at Biogem) ,lane 8. * Sequencing data on genome-miner: /media/SeqStore2/120608_SN1001/BSPP == Sample indexes == {| {{table}} | align="center" style="background:#f0f0f0;"|'''Sample IDs''' | align="center" style="background:#f0f0f0;"|'''Index''' |- | GM12878||AmpR6.3.Ind73 |- | P10E3||AmpR6.3.Ind74 |- | DF2||AmpR6.3.Ind75 |- | H0||AmpR6.3.Ind76 |- | H7||AmpR6.3.Ind77 |- | H14||AmpR6.3.Ind78 |- | H16||AmpR6.3.Ind79 |- | GM12878:H0 1:1||AmpR6.3.Ind80 |} == Concatenate sequences and trim 27 bp from 5'end (on genome-miner) == * Note: Length of the raw data 110bp less /media/SeqStore2/120608_SN1001/BSPP/s_8_*_Indx73.txt | /home/kunzhang/bin/trimFastq.pl 27 83> GM12878 less /media/SeqStore2/120608_SN1001/BSPP/s_8_*_Indx74.txt | /home/kunzhang/bin/trimFastq.pl 27 83> P10E3 less /media/SeqStore2/120608_SN1001/BSPP/s_8_*_Indx75.txt | /home/kunzhang/bin/trimFastq.pl 27 83> DF2 less /media/SeqStore2/120608_SN1001/BSPP/s_8_*_Indx76.txt | /home/kunzhang/bin/trimFastq.pl 27 83> H0 less /media/SeqStore2/120608_SN1001/BSPP/s_8_*_Indx77.txt | /home/kunzhang/bin/trimFastq.pl 27 83> H7 less /media/SeqStore2/120608_SN1001/BSPP/s_8_*_Indx78.txt | /home/kunzhang/bin/trimFastq.pl 27 83> H14 less /media/SeqStore2/120608_SN1001/BSPP/s_8_*_Indx79.txt | /home/kunzhang/bin/trimFastq.pl 27 83> H16 less /media/SeqStore2/120608_SN1001/BSPP/s_8_*_Indx80.txt | /home/kunzhang/bin/trimFastq.pl 27 83> GM12878-H0 == Mapping to hg19 (on Triton cluster) == * Generate job files and submit jobs * SEmapping.template #!/bin/csh #PBS -q small #PBS -l nodes=1:ppn=2 #PBS -l walltime=12:00:00 #PBS -o [FILENAME]_SEmapping.log #PBS -e [FILENAME]_SEmapping.err #PBS -V #PBS -M nongluk6665@gmail.com #PBS -m abe #PBS -A zhang-lab cd /home/nplongthongkum/Labdir/BSPP/Noi_Data/120608_SN1001_ASM-ASCM_20120627 ./bisReadMapperSE19Triton.pl [FILENAME] 83 * generate_jobs.sh #!/bin/bash scriptname="qsub_script.sh" echo "#!/bin/bash" > $scriptname chmod +x $scriptname for f in * do if [ `expr index $f "."` -eq 0 ] then sed "s/\[FILENAME\]/$f/g" SEmapping.template > SEmapping_$f.job echo "qsub SEmapping_$f.job" >> $scriptname fi done == Summary of mapping data == {| {{table}} border = 1 | align="center" style="background:#f0f0f0;"|'''Sample IDs''' | align="center" style="background:#f0f0f0;"|'''# of reads''' | align="center" style="background:#f0f0f0;"|'''Total sequences (bps)''' | align="center" style="background:#f0f0f0;"|'''# of CpGs called''' | align="center" style="background:#f0f0f0;"|'''Read mapping rate (%)''' |- | DF2||8,943,862||983,824,820||392,505||76.96 |- | GM12878-H0||9,336,524||1,027,017,640||390,506||79.38 |- | GM12878||7,395,278||813,480,580||333,453||81.85 |- | H0||9,208,510||1,012,936,100||398,481||77.31 |- | H14||8,087,240||889,596,400||341,384||82.64 |- | H16||9,443,812||1,038,819,320||400,255||78.32 |- | H7||6,294,626||692,408,860||292,285||80.06 |- | P10E3||6,633,346||729,668,060||312,365||79.02 |} * Mapping data directory on genome-miner: /home/nplongth/Noi_scratch/120608_SN1001_ASM-ASCM_20120627/hg19.mapping
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