This is a useful paper from 2017 titled Strategies for analyzing bisulfite sequencing data. It reviews sequencing and alignment approaches, general methylome analysis, differential methylation and annotation, as well as recommending analysis platforms for non-coders. Section 4.1 discusses differential methylation methods, comparing three different methods using a simulated dataset, including as a subset of one method … Continue reading On the optimal use of methylKit
Category: bsseq
BS-seq problems – the solution
In the previous post I described a problem with BS-seq data. After much messing about I found the solution in the analysis tool methylKit. Rather than using the final output of the Bismark aligner tool (the 'coverage' or 'cytosineReport' files) you can use methylKit to process the BAM file Bismark makes in order to generate a file … Continue reading BS-seq problems – the solution
Bisulfite sequencing – bad tiles on the flowcell
Recently I've had a great deal of difficulty with some BS-seq data, which had some bad reads where the quality dropped off randomly in the middle of the sequence - this is unusual as quality issues are typically at the ends of reads. You can see this illustrated below. The poor quality reads seem to … Continue reading Bisulfite sequencing – bad tiles on the flowcell
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