Ns126:Heyn2016: Difference between revisions

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>Shicheng
>Shicheng
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==Background==
==Background==
* Epigenomic analysis detects aberrant super-enhancer DNA methylation in human cancer
* WGBS by 101 bp pair-end sequencing.
* 11 primary tumor tissue, 2 metastasis tissue and 9 normal tissues


==Method and Procedure==
==Method and Procedure==

Revision as of 22:38, 4 March 2016

Background

  • Epigenomic analysis detects aberrant super-enhancer DNA methylation in human cancer
  • WGBS by 101 bp pair-end sequencing.
  • 11 primary tumor tissue, 2 metastasis tissue and 9 normal tissues

Method and Procedure

Sample

SRA Download

SRA to Fastq

Fastq to Bam

Bam to Hapinfo

  • Bam File Directory
TSCC: /home/ddiep/dinh_working/Bellvitge_BRI_WGBS/methylfiles/BAMfiles
Genome-miner:  /media/LTS_60T/Dinh/WGBS_LTS33/Hg19/Estellar_Bellvitge/BAMfiles
  • Bam to hapinfo


Haploinfo to Methylation Haplotype Block (MHB)

Hapinfo to Methylation Haplotype Load

trim_glore

Alignment