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richardmleggett / nextclip

Nextera Long Mate Pair analysis and processing tool
GNU General Public License v3.0
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Junction adapter detection #5

Open ctxchris opened 10 years ago

ctxchris commented 10 years ago

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

nextclip_trimming_junction_adapter

richardmleggett commented 10 years ago

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