Closed Shicheng-Guo closed 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
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.
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