Katherine Silliman commented on the post, Data Analysis – Continued O.lurida Fst Analysis from GBS Data, on the site Sam's Notebook 2 months, 3 weeks ago
Nice job getting vcftools to run! Are you using the vcf file that pyrad outputs, or ipyrad? Pyrad will output a VCF file with all variant sites, while ipyrad will output a VCF file with ALL sites variant and invariant. In either case, you want to thin your VCF to 1 variant site per GBS loci when looking at mean FST. In the notebook you are looking…[Read more]
Thanks for all of this! Much appreciated!
VCF was generated from PyRad with no alterations.
Mincov setting in PyRad was 4.
Thanks for the Biostar link; I think I’ve looked at that (and the other thread linked in that post) a few times.
I’ll check out your other notebooks; thanks!
I’ll also look into running Stacks’ “Populations”…[Read more]
Did you use 10mM DNTPs or 1mM? For the prepscale PCR it should either be 20 uL of 1mM or 2 uL of 10mM per sample.
It doesn’t look good. In the Matz 2b rad protocol, they recommend keeping cycles below 15 otherwise you see a loss in heterozygosity.
If the pCR isn’t working, then it’s because there aren’t many fragments with adaptors. The Matz protocol has an overnight…[Read more]