These are chat archives for dereneaton/ipyrad

18th
Jul 2017
nclowell
@nclowell
Jul 18 2017 00:41
@dereneaton Do you know if "remove duplicates" uses the clustering similarity threshold to determine what are "duplicates", and can you please point me to where I can read about the "remove duplicates" algorithm? I ran a branching assembly where I varied only the clustering similarity threshold from 76%-98% with the hopes of picking a good parameter value for my data by minimizing the percentage of loci lost due to "remove duplicates," as a sign of over-splitting my loci. However, I saw an unexpected pattern where the percentage of loci lost due to "remove duplicates" increased with clustering similarity, but dropped off after 95%. I figured it would only increase with clustering similarity. Thoughts? Thanks!
Nikki Phair
@phair_nikki_twitter
Jul 18 2017 13:02
@dereneaton , thanks for the speedy reply. We will definately be testing out iPyRad over the next few days. Hopefully it will help us out with some of our issues.
Zahra
@nematiz
Jul 18 2017 16:45
Hi @isaacovercast Yes I restarted it with the -f but I still get the same error.
Isaac Overcast
@isaacovercast
Jul 18 2017 18:01
@nematiz Ok, I can reproduce this error on one of my datasets. I'll work on it.
Zahra
@nematiz
Jul 18 2017 19:21
@isaacovercast thanks!