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!
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!
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