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
- Table 2.
File | title | geo_accession | status | organism_ch1 | treatment_protocol_ch1 | description.1 | data_processing |
GSM1279516_CpGcontext.Brain_W.txt.gz | GSM1279516 | Brain_white matter | GSM1279516 | Normal | sample type: Primary | Brain_WNT | SRX381706 |
GSM1279517_CpGcontext.Breast.txt.gz | GSM1279517 | Breast_normal | GSM1279517 | Normal | sample type: Primary | Breast_NT | SRX381631 |
GSM1279518_CpGcontext.CD19.txt.gz | GSM1279518 | Blood_B-cells_CD19 | GSM1279518 | Normal | sample type: Primary | CD19_NT | SRX381725 |
GSM1279519_CpGcontext.Colon.txt.gz | GSM1279519 | Colon_normal | GSM1279519 | Normal | sample type: Primary | Colon_NT | SRX381553 |
GSM1279520_CpGcontext.Colon_M.txt.gz | GSM1279520 | Colon_metastasis | GSM1279520 | Metastasis | sample type: Primary | Colon_MC | SRX381585 |
GSM1279521_CpGcontext.Colon_P.txt.gz | GSM1279521 | Colon_cancer | GSM1279521 | Cancer | sample type: Primary | Colon_PC | SRX381569 |
GSM1279522_CpGcontext.H1437.txt.gz | GSM1279522 | Lung_H1437 | GSM1279522 | Adenocarcinoma | sample type: Cell line | H1437_LCC | SRX381716 |
GSM1279523_CpGcontext.H157.txt.gz | GSM1279523 | Lung_H157 | GSM1279523 | Squamous cell cancer | sample type: Cell line | H157_LCC | SRX381719 |
GSM1279524_CpGcontext.H1672.txt.gz | GSM1279524 | Lung_H1672 | GSM1279524 | Small cell lung cancer | sample type: Cell line | H1672_LCC | SRX381722 |
GSM1279527_CpGcontext.Lung.txt.gz | GSM1279527 | Lung_normali | GSM1279527 | Normal | sample type: Primary | Lung_NT | SRX381713 |
GSM1279532_CpGcontext.U87MG.txt.gz | GSM1279532 | Brain_U87MG | GSM1279532 | Glioma | sample type: Cell line | U87MG_BC | SRX381701` |
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 MethylFreq
MF to Wig
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/bam perl ~/bin/bam2hapInfo2PBS.pl ../SaminfoPre4hapinfo.txt submit nonbismark 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:File:Heyn2016.R0.5.methyblock.bed.txt
- 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 frequency(MF)
perl ~/bin/hapinfo2mf-Estellar.pl ./ > ../Estellar2016.hapinfo2mf.txt
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%