should the input .bam be merged?

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Mackenzie Gavery

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Nov 19, 2015, 1:03:26 PM11/19/15

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Hi,

I have RRBS data for 20 individuals (n=10 per treatment). I am wondering if I should run BisSNP on each .bam separately, or if I would be better to merge them up front? I am still trying to figure out how the downstream analysis would work (e.g. identifying differential methylation or SNPs between treatments?), so I don't know what way would be best. Also, if you have any suggestions for downstream analysis (I have currently been using methylKit to identify DMR, would that still be compatible? I would appreciate it.