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Is read trimming needed for WGBS (bisulfite) data?

These days read trimming is generally unnecessary in both DNA and RNAseq. Is there any reason why the same shouldn't be true of bisulfite-treated WGBS data?

FWIW, we're typically using biscuit for alignments (https://github.com/zwdzwd/biscuit), which is based on bwa-mem.

wgbs bisufite trimming alignment
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updated by Devon Ryan Devon Ryan • written by Chris Miller Chris Miller

1 answer

Yes, we typically trim reads for WGBS even when using local alignment (bwa-meth in our case). The primary reason is that coverage for WGBS tends to be low-ish and we don't want to chance parts of the adapter getting aligned and used for methylation extraction. With fastp and recent cutadapt changes (it's finally multithreaded) at least the trimming step doesn't take seemingly forever anymore.

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written by Devon Ryan Devon Ryan

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