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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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Mappability decreased after version update. #21

Open Moonju411 opened 5 years ago

Moonju411 commented 5 years ago

Hi, I have a question about mappability decreased after version changed.

At first, I did mapping with BSseeker2 v2.0.10, Bowtie2 v2.3.1 in local alignment mode, allowing 4 mismatches, and 30-500bp fragment length after trimming with trim galore v0.4.1. By mapping with this condition, sample's average mappability was 60-80%.

Recently, I installed all related program as newest version, BSseeker2 v2.1.5, Bowtie2 v2.3.4.2, trim galore v0.5.0 and did mapping in same condition with same samples. But in this condition, average mappability dropped into 45-60%.

What can be the problem with this? How can I raise mappability?

I will really appreciate with your help!

guoweilong commented 5 years ago

Can you paste your full commands? Then I may help to figure it out.

As you know, BS-Seeker2 is very versatile and supports several modes for running and full access to parameters. Changes in parameters (even build-in parameters) can have different results: the difference lies how strict you want to do the mapping. Mappability and mapping accuracy are balanced. For RRBS, mappability of 45-60% seems good to me.

Best, Weilong