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Interactive assembly and analysis of RAD-seq data sets
Jan 25 2017 13:15 UTC
, is it possible to run ipyrad with the two-enzyme GBS method (single-end reads) according to Poland et al.?
Jan 25 2017 15:31 UTC
Yes, ipyrad should have no problem with it. I think the appropriate settings in ipyrad for this would be:
datatype = ddrad
restriction_overhang = TGCAG,CCGG
I haven't been able to replicate this problem. The sample is properly removed when I try. Can you provide any more information? Perhaps if you email me your JSON file I can find the problem.
Jan 25 2017 15:33 UTC
thanks for looking into it. I have worked around the problem by removing the sample from the barcodes file, but I'll find that run and email that json
Jan 25 2017 15:38 UTC
thank you, I will try that