Ns126:Heyn2016: Difference between revisions
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>Shicheng |
>Shicheng (→Sample) |
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*ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/ | *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 | *paired-end DNA sequencing (two reads of 100 bp each) using the Illumina HiSeq 2000 | ||
{|style="font-size:80%;" | |||
|align="left" style="background:#f0f0f0;"|''' title''' | |||
|align="left" style="background:#f0f0f0;"|''' geo_accession''' | |||
|align="left" style="background:#f0f0f0;"|''' organism_ch1''' | |||
|align="left" style="background:#f0f0f0;"|''' treatment_protocol_ch1''' | |||
|align="left" style="background:#f0f0f0;"|''' description.1''' | |||
|align="left" style="background:#f0f0f0;"|''' data_processing''' | |||
|align="left" style="background:#f0f0f0;"|''' relation''' | |||
|align="left" style="background:#f0f0f0;"|''' MF''' | |||
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| 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 | |||
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| | |||
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|} | |||
===SRA Download=== | ===SRA Download=== |
Revision as of 19:24, 28 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
- 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/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%