Open AbRawoof opened 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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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??