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PengNi / ccsmeth

Detecting DNA methylation from PacBio CCS reads
BSD 3-Clause Clear License
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calling modifications on Pacbio Revio platform #42

Open eric-hy opened 1 year ago

eric-hy commented 1 year ago

Dear authors, thanks for your great tool 'ccsmeth'. I try calling modifications on a hifi.bam generated from Pacbio Revio platform. However, I only get a empty bam files. I have noticed the given models are trained using PacBio Sequel II reads, I wonder whether differences between the two platforms leads to my results. I look forward to your reply!

PengNi commented 1 year ago

Hi @eric-hy , sorry for the delay. To call methylation using ccsmeth, the input data (hifi.bam) must contain the kinetics signals (i.e., containing TAGs such as fi, fp,ri, rp in each item of the bam file). Also, please add --no_decode in the call_mods command for the Revio dataset. For more information, pleash check issue #40 .

Best, Peng