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zhou-lab / biscuit

BISulfite-seq CUI Toolkit
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C&T Counts from biscuit vcf2bed? #10

Open timpeters82 opened 7 years ago

timpeters82 commented 7 years ago

Hi Wanding, Nice work on biscuit. Is there an option for vcf2bed to call methylated and unmethylated reads instead of just the ratio? Or do I have to parse the vcf itself for this? Cheers, Tim

zwdzwd commented 7 years ago

Hi Tim, Maybe you could use -c to get coverage (and recover from that the methylated and unmethylated reads). That coverage is the sum of methylated and unmethylated reads (the effective cytosine coverage). Usually I just use coverage and beta. I will keep in mind and make that optionally available in the next commits.

Thanks,

Wanding

timpeters82 commented 7 years ago

Thanks Wanding, that should be sufficient. Cheers, Tim