BOWTIE2: How to randomly map a read to single alignment when read is multimapping?

[cbaudo]

I want to keep only one alignment per read, so if a read maps equally well to several locations, one location should be chosen at random. Could you help me identify the option to use in Bowtie2 to execute this?

Thank you,
CB

[GenoMax]

 -k <int>           report up to <int> alns per read; MAPQ not meaningful

Does not explicit say that it would be a random location.

With BBMap you can specify ambig=random.

[cbaudo]

Many thanks

[cbaudo]

@GenoMax

Could you suggest a PacBio aligner that is capable of doing this as well?

[GenoMax]

You can use mapPacBio.sh from BBMap to align pacbio data (ambig=random should work there).

PacBio has blasr for alignment. It probably has an option to do what you want.

[Roy]

-k 1 is not a good idea. From the manual: "Bowtie 2 does not "find" alignments in any specific order, so for reads that have more than N distinct, valid alignments, Bowtie 2 does not garantee that the N alignments reported are the best possible in terms of alignment score." So -k 1 will just report the first alignment it comes across, not the best one. This is almost certainly not what you want.

Actually the requested behaviour is the default - Bowtie2 reports the best alignment it can find, and if multiple equally-good alignments are found it picks one at random, and sets a low mapq score (as the alignment is not unique).

For blasr, you probably want the option -hitPolicy randombest.

BWA mem can also map PacBio reads (use the option -x pacbio). Like Bowtie2, the desired behaviour is the default.