Hi,
I am trying to analyse Whole genome bisulfite sequencing data of Rice, but it is having biological replicates in the samples, which tool is good for this. I am very new to this field and have heard about Bismark, which was for no replicated data. Please tell me about any tool to analyse replicates.
Bismark is an aligner and methylation extractor. Are you asking about alignment (bismark works fine, it's just slow) or the actual analysis, for which bismark isn't used?