Ns126:Heyn2016

From ZhangLabWiki
Revision as of 21:40, 28 March 2016 by >Shicheng (→‎Sample)
Jump to navigation Jump to search

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

Title geo_accession organism_ch1 treatment_protocol_ch1 description.1 data_processing relation MF
GSM1279516 Brain_white matter Normal sample type: Primary Brain_W SRX381706 Bisulfite-Seq ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1279nnn/GSM1279516/GSM1279516_CpGcontext.Brain_W.txt.gz
GSM1279517 Breast_normal Normal sample type: Primary Breast SRX381631 Bisulfite-Seq ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1279nnn/GSM1279517/GSM1279517_CpGcontext.Breast.txt.gz
GSM1279518 Blood_B-cells_CD19 Normal sample type: Primary CD19 SRX381725 Bisulfite-Seq ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1279nnn/GSM1279518/GSM1279518_CpGcontext.CD19.txt.gz
GSM1279519 Colon_normal Normal sample type: Primary Colon SRX381553 Bisulfite-Seq ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1279nnn/GSM1279519/GSM1279519_CpGcontext.Colon.txt.gz
GSM1279520 Colon_metastasis Metastasis sample type: Primary Colon_M SRX381585 Bisulfite-Seq ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1279nnn/GSM1279520/GSM1279520_CpGcontext.Colon_M.txt.gz
GSM1279521 Colon_cancer Cancer sample type: Primary Colon_P SRX381569 Bisulfite-Seq ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1279nnn/GSM1279521/GSM1279521_CpGcontext.Colon_P.txt.gz
GSM1279522 Lung_H1437 Adenocarcinoma sample type: Cell line H1437 SRX381716 Bisulfite-Seq ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1279nnn/GSM1279522/GSM1279522_CpGcontext.H1437.txt.gz
GSM1279523 Lung_H157 Squamous cell cancer sample type: Cell line H157 SRX381719 Bisulfite-Seq ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1279nnn/GSM1279523/GSM1279523_CpGcontext.H157.txt.gz
GSM1279524 Lung_H1672 Small cell lung cancer sample type: Cell line H1672 SRX381722 Bisulfite-Seq ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1279nnn/GSM1279524/GSM1279524_CpGcontext.H1672.txt.gz
GSM1279527 Lung_normali Normal sample type: Primary Lung SRX381713 Bisulfite-Seq ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1279nnn/GSM1279527/GSM1279527_CpGcontext.Lung.txt.gz
GSM1279532 Brain_U87MG Glioma sample type: Cell line U87MG SRX381701 Bisulfite-Seq ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1279nnn/GSM1279532/GSM1279532_CpGcontext.U87MG.txt.gz
  • 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 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/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 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%

MHL