Question: Is read trimming needed for WGBS (bisulfite) data?
0
gravatar for Chris Miller
29 days ago by
Chris Miller21k
Washington University in St. Louis, MO
Chris Miller21k wrote:

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.

ADD COMMENTlink modified 22 days ago by Devon Ryan93k • written 29 days ago by Chris Miller21k
1
gravatar for Devon Ryan
22 days ago by
Devon Ryan93k
Freiburg, Germany
Devon Ryan93k wrote:

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.

ADD COMMENTlink written 22 days ago by Devon Ryan93k
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