Currently Reindeer will skip any queried sequence with Ns. However, I was wondering if would instead be possible to only skip any kmers with Ns (or actually, to output a count of 0 for any such kmers, in order to maintain the positions in the original query sequence). For example, bcalm can run on sequences with N's and it will simply skip any kmers that overlap N. Thanks for your consideration.
Hello,
Currently Reindeer will skip any queried sequence with Ns. However, I was wondering if would instead be possible to only skip any kmers with Ns (or actually, to output a count of 0 for any such kmers, in order to maintain the positions in the original query sequence). For example, bcalm can run on sequences with N's and it will simply skip any kmers that overlap N. Thanks for your consideration.