bwa reporting of multi-mapped reads

[Medhat]

[QUOTE=Brian Bushnell;134401]This is not correct - if there are two equal-scoring locations, bwa gives both a mapping score of 3 (equivalent to 50% probability), and so forth.

what about duplicate how BWA deals with duplicate , and Is it possible to give me the source of this info.

[Medhat]

what about duplicate how BWA deals with duplicate , and Is it possible to give me the source of this info.

[Brian Bushnell]

Its a random choice. Also when there are more than 1 equally "best" hits for a read the alignment gets a MAPQ of 0. When the author benchmarks the BWA tools he usually throws out alignments with MAPQ = 0 since those are random assignments.

This is not correct - if there are two equal-scoring locations, bwa gives both a mapping score of 3 (equivalent to 50% probability), and so forth.

If you want to map RNA-seq data for organisms with splicing, such as eukaryotes, bwa is not the right tool. You should use a splice-aware aligner like Tophat or BBMap.

[nk]

Great, thank you!

[sdriscoll]

Its a random choice. Also when there are more than 1 equally "best" hits for a read the alignment gets a MAPQ of 0. When the author benchmarks the BWA tools he usually throws out alignments with MAPQ = 0 since those are random assignments.

[nk]

I don't think this answers my question. I want to know how bwa decides which of the location it reports as the primary alignment.

[TiborNagy]

There is a command line argument: -R. If BWA reach this limit, stop searching further locations.

[nk]

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?