These are chat archives for dereneaton/ipyrad

2nd
Dec 2016
Mariana Mira Vasconcellos
@marimira
Dec 02 2016 01:55
Hi all, so far I have run ipyrad using demultiplexed samples only and it looks great. However, I want to start using the demultiplexing step 1 in ipyrad to compare with my demultiplexing pipeline. I have 3 pools of individuals that were sequenced paired end. The 24 barcodes I used for each pool are identical, but the index of read 2 is different for each pool. Should I include the index of read 2 in my barcodes file? I thought something like this, but I don't if it makes sense in ipyrad.
Ind01 CATCAT CGTACG
Ind02 AGTGAT CGTACG