Junction adapter detection

[ctxchris]

Hi,

after the trimming process, I find the single-junction-adapter present in quite a few sequences and I'm trying to figure out how the junction adapter detection process works.
In the example below, there's a perfetct match of the single-junction-adapter in the forward read and of its reverse complement in the reverse read. The reverse read however also contains the single-junction-adapter with one mismatch. I wonder why nextclip preferred to put the read pair into category B instead of trimming the perfect adapter matches from each read and putting the into category A. Is this just an unfortunate coincidence or justified behaviour?

Thank
chris

[richardmleggett]

Hi Chris,

That is an unfortunate coincidence and not something I've seen before. But it does make me realise I need to tighten up the algorithm to spot cases like this. I'll try and do it soon.

Thanks,
Richard