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
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?