These are chat archives for dereneaton/ipyrad

11th
Oct 2018
Jamie Bucholz
@Buch_research_twitter
Oct 11 2018 13:49
@isaacovercast I'm having some trouble demultiplexing my Best RAD data with ipyrad due to an "N" at the second position of most of my barcode reads not unlike the issue seen here: https://rdtarvin.github.io/RADseq_Quito_2017/main/2017/08/02/afternoon-ddRAD-pyrad.html. Unfortunately, I use 96 unique adaptors, and some are only variable by 1 nucleotide, so I cannot change the parameter files to allow 1 mismatch in the barcode file, or some reads will get lumped together that shouldn't. Is there any way to remedy this situation?
Isaac Overcast
@isaacovercast
Oct 11 2018 22:04
@Buch_research_twitter I can think of a couple ways of doing this, but none of them are going be very straightforward. Of course if there are barcode sequences that only differ at the 2nd base position then theres nothing to be done. It could be possible to write a script or hack the ipyrad code to only take account of differences at positions other than the second bp , but this could take a little work.
If only some of them differ by only one bp, there might be another trick, but if it's like 20-30% it might be just as much of a hassle.
Jamie Bucholz
@Buch_research_twitter
Oct 11 2018 23:08
@isaacovercast I was afraid you were going to say that. Thanks for the prompt response!