These are chat archives for dereneaton/ipyrad

24th
Dec 2016
Deren Eaton
@dereneaton
Dec 24 2016 19:28
Hi @Cycadales_twitter, you can filter to remove missing data by either setting a higher value for the min_samples_locus parameter, so that only loci shared across at least N samples are retained in the data set; or, you use the new popfile feature to set multiple min_samples_locus settings which apply to separate populations, which you define. The latter can be used, for example, if you wanted to only keep loci that had data for at least 3 individuals in each of your populations/species/clades.
James Clugston
@Cycadales_twitter
Dec 24 2016 23:08
Hi @dereneaton ahh ok that sounds like it will save loads of time. So If I am getting this right if I have 72 samples in an assembly and I set the min_samples_locus to say 36 then I am filtering out allowing for min 50% loci shared across samples or 58% or around 80%? Can I ask what you mean by new popfile feature to set multiple min_samples_locus settings which apply to separate populations? This would make it much more simple to be honest. Thank you for getting back to me and have a good Christmas