Find all locations of aligned reads with MQ (Mapping Quality) = 0.

Question

[captainlabman]

I have white reads in BAM file with MQ = 0. I know that it means that reads align to multiple locations. I know location of one align, but can i find another location/locations in IGV? If IGV can't do something like that, there are any another solutions?

Answer 1

[ATpoint]

Typically the aligner only reports one location (a random one) for MAPQ=0 reads. In bwa mem you can force to output every possible lolcation by adding the -a flag. IGV just reads the BAM, it does not do or infer any mapping or position itself.

Answer 2

[Brian Bushnell]

Using BBTools:

reformat.sh in=mapped.bam out=multi.bam maxmapq=3

That will give you all the alignments with a mapq of at most 3, then you can look at them in IGV to see only the multi-mapping locations. Strictly speaking, anything with mapq 3 or lower could be multi-mapped since mapq=3 would correspond to 2 equally-probable locations. Depending on the aligner you can also filter based on some of the optional SAM tags, but that's less reliable.

Answer 3

[clealk]

You can try our genome browser called GW.

You can use filtering expressions on alignments (or count command), so this should be easy to do.

e.g. type 'filter mapq == 0' into the command box

• Before

• After

Also try the count command to get a summary of the results.

Hope that helps!