How much mismatch is enough and not too much?
If I want to map my reads to related genera/species (within a family) how much mismatch should I allow. Obviously, if I set no or very little mismatches I will find conserved regions among them.
The question is - how to inspect how much their genomes are similar by just mapping reads? Should I just stick to stringent criteria and just go the way -> the more similar they are, the more reads will map even with no or little mismatches?
I will do whole genome alignments, but until I get a good assembly I thought I could try it this way. No?
Thanks!
If I want to map my reads to related genera/species (within a family) how much mismatch should I allow. Obviously, if I set no or very little mismatches I will find conserved regions among them.
The question is - how to inspect how much their genomes are similar by just mapping reads? Should I just stick to stringent criteria and just go the way -> the more similar they are, the more reads will map even with no or little mismatches?
I will do whole genome alignments, but until I get a good assembly I thought I could try it this way. No?
Thanks!
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