Can a part of a read be in the alignment and in the supplementary alignment (-F 0x800) as well?
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4.0 years ago
Macspider ★ 3.4k

Hello fellow bioinformaticians,

I have a question that arises from observations in my data. I am using chimeric reads in my analysis, which I had obtained through bwa-mem and then extracting all the sam records possessing the 0x800 bit.

These records represent reads that have supplementary alignments, i.e. two parts of the read map to two different locations.

I am now computing the length of the alignment of each part, and observed two phenomena:

  • sometimes the sum of the lengths of the two local alignments (first + suppl.) doesn't add up to the read length -> this is expected because the read is aligned locally and therefore doesn't need to be mapped end-to-end

  • sometimes this sum exceeds the read length: this was not expected from me

I figured out that this could theoretically happen if, within the read, the first and the supplementary alignment have a region in common. Can this happen? Should this happen?

sequencing reads chimeric bwa supplementary • 919 views
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