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=== Bam to Hapinfo (Update: March/29/2016)=== *bam and hapinfo files * N37: /home/shg047/oasis/N37/sortBam ** cd /home/shg047/oasis/N37/hapinfo ** perl ../[[renameN37.pl]] ** rm ~/oasis/monod/hapinfo/N37* ** cp N37* ~/oasis/monod/hapinfo/ * SALK: /home/shg047/oasis/SALK/bam *2 Colon (GSE46644): /home/shg047/oasis/Ziller2013 cd /media/LTS_60T/Dinh/WGBS_LTS33/Hg19/Tumor_WGBS/BAMfiles cd /oasis/tscc/scratch/ddiep/Ziller_BAMfiles GSM1204465 SRX332736 Colon primary tumor GSM1465024 SRX669642 HCT116 cd /home/shg047/oasis/Tumor-WGBS/HCT116-SRX669642/bam perl ~/bin/[[samInfoPrep4Bam2Hapinfo.pl]] .sorted.clipped.bam > ../Saminfo4bam2hapinfo.txt perl ~/bin/[[bam2hapInfo2PBS.pl]] ../Saminfo4bam2hapinfo.txt submit nonbismark cd /home/shg047/oasis/Tumor-WGBS/HCC-SRX332736 perl ~/bin/[[samInfoPrep4Bam2Hapinfo.pl]] .sorted.clipped.bam > ../Saminfo4bam2hapinfo.txt perl ~/bin/[[bam2hapInfo2PBS.pl]] ../Saminfo4bam2hapinfo.txt submit nonbismark * Blood: ** ln -s /home/k4zhang/my_oasis_tscc/MONOD/whole_blood_WGBS/BAMfiles bam ** cd /home/shg047/oasis/AgeBlood ** perl [[~/bin/mergeBamByChrosome.pl]] /home/shg047/oasis/AgeBlood/bam /home/shg047/oasis/AgeBlood/mergeBam submit * HCC: * Plasma: **Phase I: *** where is fastq? ***/oasis/tscc/scratch/ddiep/Working/Rerun_rrbs/BAMfiles ***/oasis/tscc/scratch/ddiep/Working/Rerun_rrbs/MethylFreq **Phase II: *** where is fastq? *** /oasis/tscc/scratch/ddiep/Plasma_RRBS_151208/BAMfiles **Phase III: *** * Estellar: /home/shg047/oasis/Estellar2016
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