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nloyfer / wgbs_tools

tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies
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bam2pat-combine OT and OB? #76

Closed chang-bwl closed 1 month ago

chang-bwl commented 5 months ago

Hi, wgbstools is very convenient for processing DNA methylation data. I would like to confirm: When using bam2pat, does it merge the methylation status of CpG sites for both the OT and OB strands in the BAM file? For example, chr3 5394764 CCCC 26 represents reads starting from cpg_index 5394764, which may include the OT strand at chr3:x or the OB strand at chr3:x+1. However, it is not possible to differentiate them from the pat file, is that correct? Thanks!

yonniejon commented 1 month ago

Hi. Yes, you are correct. The pat file includes both but these cannot be differentiated from the pat file.