These are chat archives for dereneaton/ipyrad

19th
Oct 2017
Wind-ant
@Wind-ant
Oct 19 2017 02:14
Hello everyone,I want to use pyrad or ipyrad to do D-test(or ABBA-BABA),but in the web of pyrad and ipyrad,I could't find the tutorial of this method,anyone can tell me where to find it or at least all the necessary procedures and input files? Thanks
Deren Eaton
@dereneaton
Oct 19 2017 13:57
Hi @Wind-ant, you can follow this notebook to run D-tests with the API: https://github.com/dereneaton/ipyrad/blob/master/tests/workshop-abba-baba.ipynb. Some of the extended tests are still in development, but we currently support ABBA-BABA and some plotting functions.
jomare1188
@jomare1188
Oct 19 2017 18:32
hi guys, i have PE GBS data and i don't known how to start, does ipyrad manage well enough this type of data (pairgbs)? or should i merge the PE and treat them like SE (gbs)?
Deren Eaton
@dereneaton
Oct 19 2017 21:23
@jomare1188, yes ipyrad has been tested extensively with paired end gbs data and treats it quite differently from RAD or ddRAD data. It is listed under our supported data types here: http://ipyrad.readthedocs.io/files.html#supported-data-types