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  • bismark score_min; CpG cytosine?

    Hello,

    In my knowledge, one can change mapping stringency with the score_min option by adjusting mismatch/indel penalties.
    What I'm curious is whether cytosines in CpG contexts are also counted as mismatches. If so, should I give more relaxed parameters than ordinary mapping such as bowtie?

    Thank you!

  • #2
    The score_min function only adjusts the penalties for non-bisulfite mismatches. All positions involving Cs, irrespective of its methylation state, are treated as T and hence do not count towards the limit set by --score_min.

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