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PacificBiosciences / pb-CpG-tools

Collection of tools for the analysis of CpG data
BSD 3-Clause Clear License
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strand information on the output bed file #7

Closed hrrsjeong closed 2 years ago

hrrsjeong commented 2 years ago

Thanks for your effort in making this great tool! I checked the output from pb-CpG-tools and found that there's no strand information. Does the program merge the information from both strands and use the genomic coordinate of the positive strand?

rhallPB commented 2 years ago

The data is not stranded, i.e. the direction of a HiFi read is arbitrary and we detect symmetric CpG. Therefore we merge the stands in the pileup to increase the signal. Yes, coordinates are reported on the positive strand.