ERRBS Methylation data analysis

Question

[madkitty]

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 is welcome :)

Answer 1

[Shicheng Guo]

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

Answer 2

[anairlema]

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)