Read trimming in BS-Seq
In WGBS analysis, the Bismark tutorial mentions removing a few bases from the 5' and 3' end of the reads as they might result in bias (can be adjudged from M-bias plot).
In Trim galore, it is done using --clip_r1/2 and --three_prime_clip_r1/2 , as per the manual. Are CROP and HEADCROP the equivalent for trimmomatic? Should this bases be removed by default? If removed, should --ignore_r2 2 option be used with bismark_methylation_extractor .
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Arindam Ghosh
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