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

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? enter image description here

align igv bam
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updated by clealk • clealk • written by captainlabman • captainlabman

3 answers

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.

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written by ATpoint ATpoint

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.

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written by Brian Bushnell Brian Bushnell

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 enter filter command

  • After result

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

Hope that helps!

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written by clealk • clealk

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