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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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Definition to the reads which are not fully converted by bisulfite treatment? #12

Closed Shicheng-Guo closed 7 years ago

Shicheng-Guo commented 7 years ago

Hi Dr. Weilong,

Where I can find the definition to the reads which are not fully converted by bisulfite treatment?

I notice it before, however, I can not find it again when I need it.

Thanks.

Shicheng

guoweilong commented 7 years ago

Dear Shicheng,

The parameter "--XS=XS_FILTER" of bs_seeker2-align.py is to mark which reads are not fully converted by bisulfite treatment. (in BAM file, reads with tag XS:i:1) The parameter "-x, --rm-SX" of bs_seeker2-call_methylation.py is to remove the reads which are marked as not fully converted.

You can also read our paper to see how the filtering funciton works. http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-774

Best, Weilong

At 2016-11-15 02:11:08, "Shicheng Guo" notifications@github.com wrote:

Hi Dr. Weilong,

Where I can find the definition to the reads which are not fully converted by bisulfite treatment?

I notice it before, however, I can not find it again when I need it.

Thanks.

Shicheng

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