Hi guys
I was wondering whether anyone knows how the bwa aligner behaves with degenerated nucleotides. Say, for example, reference contains fifty X bases that could be any of the 4 canonical bases, and I align 50bp reads to it, should I expect all the reads will map to the X string? I have a gene as a reference, and for this gene I know the exons and the intron positions. However I do not have introns sequences. I was thinking to report 10/20 X upstream and downstream the exons in order to get more information about their beginning/ending sequence. Thanks!
I was wondering whether anyone knows how the bwa aligner behaves with degenerated nucleotides. Say, for example, reference contains fifty X bases that could be any of the 4 canonical bases, and I align 50bp reads to it, should I expect all the reads will map to the X string? I have a gene as a reference, and for this gene I know the exons and the intron positions. However I do not have introns sequences. I was thinking to report 10/20 X upstream and downstream the exons in order to get more information about their beginning/ending sequence. Thanks!
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