Question: How Does Bwa Report Multi-Mapped Reads
0
gravatar for bbio
6.0 years ago by
bbio90
United Kingdom
bbio90 wrote:

I am mapping some RNA-seq data with bwa and would like to do some analysis on where multi-mapped reads fall.

I know that I can extract multi-mapped reads by looking for mapq < 23 and/or the XA flag on the reads. However, I am wondering how bwa decides which location to report for a read that can be mapped to two different locations equally well. Does it choose a random one? Does it always report the first one? Something else?

Does anybody know what exactly bwa does here?

mapping bwa • 4.4k views
ADD COMMENTlink modified 6.0 years ago by Istvan Albert ♦♦ 82k • written 6.0 years ago by bbio90
3
gravatar for Istvan Albert
6.0 years ago by
Istvan Albert ♦♦ 82k
University Park, USA
Istvan Albert ♦♦ 82k wrote:

A random location is selected.

Also see this post, although not specifically bwa related but it goes to show that things can go wrong:

ATTENTION: bowtie2 and multiple hits

ADD COMMENTlink modified 6.0 years ago • written 6.0 years ago by Istvan Albert ♦♦ 82k

Do you have any idea if the MAPQ will be 0 in case of multiple mapping or something else? (I read two opinions about that)

ADD REPLYlink written 2.6 years ago by Medhat8.6k

The MAPQ=0 is a convention that bwa uses and not a standard.

And even considering it a convention it is not quite right. Having a multi-mapped read does not mean that the chance of the alignment being correct is zero.

The best way to detect multimapping is the check the SAM tag for alternative mappings.

ADD REPLYlink written 2.6 years ago by Istvan Albert ♦♦ 82k
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