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==Human IPS/ESC MHB== * Human hapinfo files, total 70. 1st part(59=49+10), 2nd part= 11 (ips and scnt) cd /home/shg047/work/monod/hapinfo ls *hapInfo.txt | grep -v CTT | grep -v PC | grep -v NC | grep -v LC | grep -v "\-7-" | grep -v 6- | grep -v "\-T-" | grep -v "\-P-" | grep -v merge | xargs -I {} cat {} >> merge.txt cd /home/shg047/work/Alice/human/mergeHapinfo ls *hapinfo.txt | xargs -I {} cat {} >> /home/shg047/work/Alice/human/mergeHapinfo/merge.txt # Go to GM since the memory of TSCC is not enough. cd /home/shg047/work/monod/hapinfo # already have the key, no need input the passwd scp merge.txt shg047@genome-miner.ucsd.edu:/media/Home_Raid1/shg047/work/Alice/human/hapinfo cd /media/Home_Raid1/shg047/work/Alice/human/hapinfo perl ~/bin/hapinfoMerge.pl merge.txt perl ~/bin/hapinfo2mhb.pl merge.txt.SumUniq 0.3 > mm9.MHB.0.3.txt perl ~/bin/hapinfo2mhb.pl merge.txt.SumUniq 0.5 > mm9.MHB.0.5.txt mkdir ../mhb mv mm9.MHB.0.5.txt ../mhb mv mm9.MHB.0.3.txt ../mhb wc -l /home/shg047/oasis/Alice/mouse/mhb/mm9.mhb.0.3.bed: 411551 wc -l /home/shg047/oasis/Alice/mouse/mhb/mm9.mhb.0.4.bed: 141762 wc -l /home/shg047/oasis/Alice/mouse/mhb/mm9.mhb.0.5.bed: 46675 * 417 SRR download(complete, remember fastq-dump should be updated regular or else the download will be with lots of confusing mistake) perl [[srrdownload.pl]] * 417 Alignment by bismark and BAM (complete) cd /home/shg047/work/Alice/human perl bismarkAutoSingle.pl submit * 417 sortBam(complete) cd /home/shg047/work/Alice/bam perl ~/bin/bam2sortBam.pl sortc submit * Remove cancer samples * 417 hapinfo (complete) cd /home/shg047/work/Alice/sortBam perl ~/bin/SaminfoPre4hapinfo.pl > sampleconfig.txt perl ~/bin/bam2hapInfo2PBS.pl sampleconfig.txt non bismark /home/shg047/oasis/db/hg19/hg19.chrom.sizes /home/shg047/oasis/db/hg19/HsGenome19.CpG.positions.txt * coverage, R2, methylation level WNT5A chr14:29318659-29338701 PPP3CA chr3:136333030-136600691 sort the new bam files
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