Methylation Bisulfite-Sequencing: Bismark, BS seeker, BSMAP, RMAPBS, MAQ

Question

[Shicheng Guo]

Is there any systemic evaluation to BS-seq alignment and downstream analysis? or is there any other relevant software to share or recommend?

Answer 1

[Ian]

Here are two reviews:

DNA methylome analysis using short bisulfite sequencing data: http://www.hubmed.org/display.cgi?uids=22290186

Statistical methods for detecting differentially methylated loci and regions: http://www.ncbi.nlm.nih.gov/pubmed/25278959

Answer 2

[Devon Ryan]

Most of the aligner papers have comparisons between the various aligners, though I don't know of anyone actually using MAQ for BSseq alignments (I imagine it wouldn't work well). You can find an example here and more by searching pubmed.

For down-stream analysis tools, you'd again have to look at the papers for the tools themselves. If a tool has a competitor then the paper describing it will have a comparison. Be very wary of the results of these, they may or may not be relevant to what you're working on (e.g., all of the papers use experiments that will have an absurdly large effect size).