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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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How to handle data with replicates?? #34

Open AbRawoof opened 4 years ago

AbRawoof commented 4 years ago

I have two replicates for each sample group. How should I handle replicate data. Do I need to align each of them separately ?? Is it possible to merge them in downstream analysis while calling DMS/DMRs??

BSSeeker commented 4 years ago

You can alignment them seperately. For the call-methylation step, you need to merge the bam files first. "cgmaptools dmr" will treat a group as one sample, you need to merge merge them first, such as using "cgmaptools merge tosingle" command.

Best, Weilong

At 2020-01-17 14:31:40, "AbRawoof" notifications@github.com wrote:

I have two replicates for each sample group. How should I handle replicate data. Do I need to align each of them separately ?? Is it possible to merge them in downstream analysis while calling DMS/DMRs??

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