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rrwick / Porechop

adapter trimmer for Oxford Nanopore reads
GNU General Public License v3.0
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1d^2 adapter basecalls #35

Closed joshquick closed 6 years ago

joshquick commented 6 years ago 
# But when looking at actual reads, I found two parts. The first corresponds to one end
# of the provided sequences (through slightly different):

Was talking to John Tyson about this and he pointed out that the 1d^2 adapter contains a chemical modification which is what gives it affinity to the R9.5 pore so it looks like it is throwing the basecalling off here as you observe the reads don't match the documentation. As it is quite a long adapter it probably doesn't matter but just wanted to point it out.

rrwick commented 6 years ago

That's good to know - thanks for the info!

Perhaps if the modification is in the middle of the adapter, that would explain why I tend to see the start and the end but not always the middle.