Originally posted by gene_x
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Can you help me clarify one thing? In the M-bias plot for read2, is position 1 the start of the read2? I'm a bit confused about the orientation of the read2. I thought in M-bias plot, position 1 is the the end of read2 (after read 2 is reverse complemented)? probably my understanding was wrong...
Also, in M-bias plot for read2, the first 2 bases have much lower average CpG methylation, that suggests they should be ignored in the downstream analysis? I could use the -ignore_r2 option in methylation extractor to do it?
Thanks!
Thanks!
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