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BSSeeker / BSseeker2

A versatile aligning pipeline for bisulfite sequencing data
http://pellegrini.mcdb.ucla.edu/BS_Seeker2/
MIT License
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Duplication #20

Closed hyystvar closed 5 years ago

hyystvar commented 5 years ago

I do not find the step of removing PCR duplication in your RRBS pipline. why?

guoweilong commented 5 years ago

We don't recommend you to use PCR duplication in RRBS, as in RRBS, reads from one region usually start from same position (such as C-CCG end), and even different moleculars would have same sequence. Thus remove duplicates sequence in RRBS is not equal to remove PCR duplication reads.

Best, Weilong