These are chat archives for dereneaton/ipyrad

Feb 2017
Feb 10 2017 01:18
@isaacovercast Hi Isaac, I have been using your easySFS for generating sfs file and I really like the program. I did not know that the program will subsample 1 random snp per locus. So if I do not use '-a' argument, it will subsample 1 random snp per locus, right? Thanks a lot!
Isaac Overcast
Feb 10 2017 19:17
Yes, that's right, the default is one snp per locus. Glad you like it.
Feb 10 2017 22:45
@dereneaton and @isaacovercast , the docs (under assembly parameters) suggest that low quality bases are converted to N during step 2, and per-read counts of Ns are subsequently used for filtering. But looking at the source I don't see this happening anywhere. cutadapt uses the quality threshold to trim poor base calls on the edges, but as far as I can tell doesn't do anything to bases on the interior of the read. In contrast, in the pyrad source (i.e., lines 158-163), there's masking of low quality bases ... are the docs wrong or am I being silly?
Deren Eaton
Feb 10 2017 22:58
@nspope you're right, we haven't updated the docs since we switched to using cutadapt.
we now trim-n from the 3' end, and filter reads for max-n (max-low-qual-bases)