These are chat archives for dereneaton/ipyrad

Jul 2017
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
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.
Jul 18 2017 16:45
Hi @isaacovercast Yes I restarted it with the -f but I still get the same error.
Isaac Overcast
Jul 18 2017 18:01
@nematiz Ok, I can reproduce this error on one of my datasets. I'll work on it.
Jul 18 2017 19:21
@isaacovercast thanks!