These are chat archives for dereneaton/ipyrad

Mar 2017
Spiros Papakostas
Mar 09 2017 08:33
I have paired-end reads of single digestion rad experiment. I am a bit confused as to the datatype flag. "rad" doesn't combine the two reads into one sample, but then "pairgbs" seems to select solely the forward reads (R1).
Emily Warschefsky
Mar 09 2017 14:28
@dereneaton - so I had already gone ahead and tried moving the files and running it to see if it would solve the problem, and it seems to have run fine now - I am recovering loci for all the individuals and not getting the NaN problem
Isaac Overcast
Mar 09 2017 17:05
@SpPapakostas_twitter The datatype should be consistent with your library prep protocol. Did you do the library prep or did you have it done by the sequencing facility? If you have paired end original RAD protocol (with the sonication step) then R2 reads won't "line up" nicely so ipyrad has trouble assembling R2. For pairgbs it should use both R1 and R2 just fine. If it's paired end gbs and r2 is getting ignored then that's a bug.