Ns126:Heyn2016: Difference between revisions

From ZhangLabWiki
Jump to navigation Jump to search
>Shicheng
>Shicheng
Line 19: Line 19:


===SRA to Fastq===
===SRA to Fastq===
===trim_glore===


=== Fastq to Bam ===
=== Fastq to Bam ===

Revision as of 23:54, 5 March 2016

Background

  • Epigenomic analysis detects aberrant super-enhancer DNA methylation in human cancer
  • WGBS by 101 bp pair-end sequencing.
  • Phred Score: 33
  • 11 primary tumor tissue, 2 metastasis tissue and 9 normal tissues

Method and Procedure

Sample

SRA Download

SRA to Fastq

trim_glore

Fastq to Bam

Bam to Hapinfo

  • Bam File Directory
TSCC-1: /home/ddiep/dinh_working/Bellvitge_BRI_WGBS/methylfiles/BAMfiles
TSCC-2: /oasis/tscc/scratch/ddiep/BAMfiles
Genome-miner:  /media/LTS_60T/Dinh/WGBS_LTS33/Hg19/Estellar_Bellvitge/BAMfiles
  • Bam to hapinfo
cd /oasis/tscc/scratch/ddiep/BAMfiles
perl ~/bin/SaminfoPre4hapinfo.pl > ~/oasis/Estellar2016/SaminfoPre4hapinfo.txt
cd /home/shg047/oasis/Estellar2016/hapinfo
perl ~/bin/bam2hapInfo2PBS.pl ../SaminfoPre4hapinfo.txt
qsub SRX381621_tumor_breast.chr20.job
  • Merge hapinfo in different chrosome to one file by sample ID
cd /home/shg047/oasis/Estellar2016/hapinfo
perl ~/bin/hapinfoMergeByChrosome.pl
cd /home/shg047/oasis/Estellar2016/mergeHapinfo

Haploinfo to Methylation Haplotype Block (MHB)

Hapinfo to Methylation Haplotype Load

cd /home/shg047/oasis/Estellar2016/mergeHapinfo
perl ~/bin/hapinfo2mhl.pl
qsub hapinfo2mhlPBS.job

Alignment