These are chat archives for dereneaton/ipyrad

3rd
Oct 2017
congliu0514
@congliu0514
Oct 03 2017 00:57
Hi @dereneaton @isaacovercast I am recently running lots of ipyrad to test the best parameters setting for our upcoming large phylogenetic analysis. One idea was to set the max_alleles_consens=1 for our diploid samples to get rid of the within-sample variation. So I ran ipyrad with max_alleles_consens=1 and got almost double the number of loci compare to max_alleles_consens=2. Do you guys know why the number of loci was doubled by using max_alleles_consens=1? Thanks a lot !!
rfolkert
@rfolkert
Oct 03 2017 17:12

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 [28] and instead use:

12  ## [21] [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