How is downstream analysis impacted for non-directional bisulfite-sequencing libraries aligned in non-directional mode with biscuit?

zhou-lab / biscuit

BISulfite-seq CUI Toolkit

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How is downstream analysis impacted for non-directional bisulfite-sequencing libraries aligned in non-directional mode with biscuit? #40

Open meb326 opened 4 years ago

meb326 commented 4 years ago

I have non-directional bisulfite sequencing libraries that I aligned with biscuit. I am wondering how this will influence methylation calls in biscuit pileup-->vcf2bed and biscuit epiread.