Ns126:Heyn2016

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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)

cd /home/shg047/oasis/Estellar2016/mergeHapinfo
cat *.hapInfo.txt >> HapinfoMerge.txt
perl ~/bin/hapinfo2mhb.pl HapinfoMerge.txt 0.4 > Heyn2016.R0.4.methyblock.bed
perl ~/bin/hapinfo2mhb.pl HapinfoMerge.txt 0.5 > Heyn2016.R0.5.methyblock.bed
perl ~/bin/hapinfo2mhb.pl HapinfoMerge.txt 0.6 > Heyn2016.R0.6.methyblock.bed
perl ~/bin/hapinfo2mhb.pl HapinfoMerge.txt 0.7 > Heyn2016.R0.7.methyblock.bed
qsub hapinfo2mhb.job
bedtools intersect -wa -u -a ../../monod/mhb/WGBS_pooled_mappable_bins.all_autosomes.mld_blocks_r2-0.5.bed -b Heyn2016.R0.5.methyblock.bed | wc -l 
bedtools intersect -wa -u -a Heyn2016.R0.5.methyblock.bed -b ../../monod/mhb/WGBS_pooled_mappable_bins.all_autosomes.mld_blocks_r2-0.5.bed | wc -l 
wc -l ../../monod/mhb/WGBS_pooled_mappable_bins.all_autosomes.mld_blocks_r2-0.5.bed
  • 73976 Heyn2016.R0.5.methyblock.bed
  • 71697 of 147888 within Heyn2016.R0.5.methyblock.bed
  • 73976 of Heyn2016.R0.5.methyblock.bed within 147888
  • MHB identified by Heyn2016 dataset 100% located within our previous defined MHBs

Hapinfo to Methylation Haplotype Load

cd /home/shg047/oasis/Estellar2016/mergeHapinfo
perl ~/bin/hapinfo2mhl.pl ./ >  Estellar2016.MHL.txt
qsub hapinfo2mhlPBS.job
* Estellar2016.MHL.txt
* 22 samples
* 147314 MHB
* missing ratio: 19.01826%

Alignment