ERRBS Methylation data analysis
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5.9 years ago
madkitty ▴ 620

We had 6 samples, 3 controls and 3 tumors, for which we ordered whole bisulfite sequencing, we're interested in knowing the changes between the two control/tumor. Though the sequencing facility did by mistake a ERRBS targeted sequencing. We decided to go with it, unfortunately I've never analyzed that kind of sequences. I have access to the SAM files on our server. 

  • What would you do to analyze this methylation data, where to start, what to look for? 
  • Any recommendation of packages/software publicly available? 

 

Any input are welcome :) 

methylation ERRBS Bisulfite next-gen homer • 2.2k views
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Entering edit mode
5.9 years ago
Shicheng Guo ★ 8.8k

You can try the following two method:

  • DMAP: differential methylation analysis package for RRBS and WGBS data.
  • BSmooth is a pipeline for analyzing WGBS data: aligning, quality control, and identifying DMRs.

More information see: Gallery: Computational tools for DNA methylation

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14 months ago
anairlema • 0

We usually perform ERRBS data analysis using this workflow: -trimming using cutadapt -Alignment using Bismark - CpG.txt file generation on Methylkit or bedgraph generation with methyldacker -Statistics on methylkit package -DMCs and DMRs using methylSig package -alternatively you can use methylkit+ eDMR package to find DMRs

You can find a lot of information here: http://www.bioinformatics.babraham.ac.uk/projects/bismark/RRBS_Guide.pdf about alignment and on Bioconductor for methylkit and methylsig (https://www.bioconductor.org/packages/release/bioc/vignettes/methylKit/inst/doc/methylKit.html https://www.bioconductor.org/packages/release/bioc/vignettes/methylSig/inst/doc/using-methylSig.html)

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