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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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Remove overlapped region between two mates for paired-end reads #8

Closed haodongchen closed 8 years ago

haodongchen commented 8 years ago

It seems that now BSseeker2 supports the removal of overlapped regions between two paired-end reads (--rm-overlap) in bs_seeker2-call_methylation.py. Does it only remove the overlapped region between reads, or completely remove the second read if overlapped with the first one?

guoweilong commented 8 years ago

Haodong,

BS-Seeker2 has been supporting --rm-overlap for a long time.

It will remove overlapped region between reads, NOT removing whole reads.

Best, Weilong

At 2016-05-13 05:10:13, "Haodong Chen" notifications@github.com wrote:

It seems that now BSseeker2 supports the removal of overlapped regions between two paired-end reads (--rm-overlap) in bs_seeker2-call_methylation.py. Does it only remove the overlapped region between reads, or completely remove the second read if overlapped with the first one?

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haodongchen commented 8 years ago

Thank you for clarification, Weilong. Could you please update the README.md file to reflect this change? Thanks!

guoweilong commented 8 years ago

Thanks for this suggestion. I'll update the README in the next few days.

Best, Weilong

At 2016-05-14 02:06:06, "Haodong Chen" notifications@github.com wrote:

Thank you for clarification, Weilong. Could you please update the README.md file to reflect this change? Thanks!

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