BWA and X bases

scami

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#1

BWA and X bases

02-24-2014, 06:44 AM

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!
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Brian Bushnell

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#2

02-24-2014, 10:39 AM

No, no sequence will map exclusively to N or X with BWA (or any other aligner I've used). A read can extend into N or X, but it has to match a seed sequence outside of the masked area.
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scami

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#3

02-24-2014, 11:16 AM

Thanks!

Thank you very much for your reply. This is a good news for the project I had in mind.
Cheers
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