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
- assemble sample config file
- ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/
- paired-end DNA sequencing (two reads of 100 bp each) using the Illumina HiSeq 2000
SRA Download
- SRA: ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP%2FSRP033%2FSRP033252
- GEO: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE52271
- GEO Download: ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE52nnn/GSE52271/suppl/
- GEO Download: ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE52nnn/GSE52272/suppl/
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
Hapinfo to Methylation Haplotype Load
cd /home/shg047/oasis/Estellar2016/mergeHapinfo perl ~/bin/hapinfo2mhl.pl qsub hapinfo2mhlPBS.job