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#93 Slight modification to incorporate methylation data
Hello,
For aligning methyl seq data we have to convert the C to T in end 1 reads and G to A in the end 2 reads and align against a three letter coded genome. Its easy to make the three lettered genome.
I would really appreciate if the authors could provide a simple flag which would convert the C to T for end 1 and G to A for end 2 for the reads before doing the alignment. This would help both in doing RRBS and whole genome alignments.
regards,
Rahul