pat result for short fragments (<150)

nloyfer / wgbs_tools

tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies

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pat result for short fragments (<150) #4

Closed WRui closed 2 years ago

WRui commented 2 years ago

Hi, I wonder if the fragment is short(<150bp) and R1 and R2 are fully overlapped(2*150 pair-end data), if R1 and R2 (with the same read id )showed different methylation level, what the pat file would output, it will output two different rows or just output one rows that only use methylation levels of R1 or R2?

nloyfer commented 2 years ago

Hi, Read pairs are always concatenated and considered as a single fragment. If there is overlap, and there are CpGs with different methylation statuses between the two reads, we output . for these CpGs (i.e. missing value).