Ns126:Heyn2016: Difference between revisions

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


=== Haploinfo to Methylation Haplotype Block (MHB) ===
=== Haploinfo to Methylation Haplotype Block (MHB) ===

Revision as of 23:31, 4 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

SRA Download

SRA to Fastq

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

Haploinfo to Methylation Haplotype Block (MHB)

Hapinfo to Methylation Haplotype Load

trim_glore

Alignment