These are chat archives for dereneaton/ipyrad
Hi Deren and Isaac
I am having some trouble with the pop_assign_file using it for assigning min_sample_locus. I have 14 populations, with 24 individuals each.
These are the last lines of my pop_assign_file:
Vam020 Vam Tou011 Tou # Pal:12 Vam:12 Man:12 Kru:12 Ned:12 Rad:12 Sov:12 Urw:12 Gim:12 Lit:12 Hor:12 MsV:12 Ven:12 Tou:12
The problem is that by using this, I only retain a few shared loci (~100) per population, but when I remove this line and the info for  and instead use:
12 ##  [min_samples_locus]: Min # samples per locus for output
*edit, I just figured out this would probably mean 12 loci across all my 336 individuals.
But still, when I run a complete analysis for each population separately, I retain many more loci (~10:000). What am I doing wrong here? Can you explain the difference?
Thank you, Remco