Bowtie SAM XM

[Bio.X2Y]

Hi,

I think I've come across a small bug in Bowtie in relation to its SAM output.

The manual says that when the number of matches for a read exceeds a user threshold (-m), the XM optional tag on the corresponding SAM line will be "m+1". However, in practice this seems to be just "m". I'm using version 0.12.5.

Ben, if you're out there, how would you prefer reports like this to be made? (email, seqanswers, etc.?)

Cheers.

[Ben Langmead]

Hi Bio,

Yes, great catch. When -m is used, the XM tag for the reads that were filtered due to -m have m instead of m+1. Note that the XM tag has the correct for randomly-selected alignments in -M mode; this only affects runs where -S and -m are set.

I'll have a fix in the next version. Sourceforge is a good place for bug reports (see link from Bowtie site).

Thanks,
Ben

[Bio.X2Y]

Thanks Ben