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BSSeeker / BSseeker2

A versatile aligning pipeline for bisulfite sequencing data
http://pellegrini.mcdb.ucla.edu/BS_Seeker2/
MIT License
61 stars 25 forks source link

Disclaimer for methylation call maximum methylation depth of 8000 #39

Open villars4 opened 3 years ago

villars4 commented 3 years ago

I just would like to advocate for either: 1) a prominent disclaimer stating that the default maximum depth used during methylation calling can create misleading methylation calls. 2) removing this maximum depth default parameter

All the best, Severiano

guoweilong commented 3 years ago

Thanks for your suggestion. Actually, the data structure implemented in C language has the limitation for ~8000 (8192-1). For most site, the coverage should be very low (<100). Maybe for plastid genome or repeat regions, you may find some position with coverage exceeding the maximum limitation. For these cases, I suggest users to be careful with the result, or to write custom codes.

Best, Weilong

At 2021-03-03 00:53:26, "villars4" notifications@github.com wrote:

I just would like to advocate for either:

a prominent disclaimer stating that the default maximum depth used during methylation calling can create misleading methylation calls. removing this maximum depth default parameter

All the best, Severiano

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