These are chat archives for dereneaton/ipyrad

Jun 2018
Jun 19 2018 10:10

Hello @dereneaton and @isaacovercast . I'm using ipyrad to analyze some 2bRAD data but I'm stuck at the very beginning.
I want to do the demultiplexing but I can't find a way to set the restriction_overhang parameter correctly. Digestion was made with BsaXI which has this recognition site pattern:
N{12}ACN{5}CTCCN{10} --> 33bp

Reads are adapter free, just:
5'insert+barcode3' (33+8=41bp long)

After running step 1, the stats file shows plenty of "cut_found" but barely any "bar_matched".
Barcodes's file is present and consist of name(TAB)sequence with one barcode per line, as expected.

Any suggestion on how to correctly enter the overhang pattern?
Thank you.

Jun 19 2018 13:33

Hi @isaacovercast, @dereneaton.
I have a question regarding the abba-baba-cookbook.ipynb; specifically regarding the interpretation of the output.
I used the notebook to compute a partitioned D-statistics analysis test by defining 5 populations. The output table has 3 lines per test, p3, p4 and shared.

I assume that the values in the 'shared' line correspond to D12 and Z12 values respectively. I would like to know whether the line for p3 corresponds to the tested patters : ABBAA vs. BABAA and therefore D1. Consequently p4 would equate to the test D2 and ABABA vs BAABA. Or is it vice verca?.

Thank You and Cheers from Germany