These are chat archives for dereneaton/ipyrad

May 2018
Isaac Overcast
May 09 2018 13:45
@insectnate What version of ipyrad are you running? Your params file is from a very old version.
Can you make sure you're on the most recent version (v.0.7.24). You can upgrade like this: conda install -c ipyrad ipyrad. If you are on the most recent version, i would recommend creating a new params file anyway ipyrad -n whatever and then copying over the info from this old params file.
If you were using an old version, and then you updated to the new version and now you're seeing this error it could be that an old version of the assembly .json is hanging around and is incompatible with the new version. You could also try running step 1 with the -f flag do overwrite any (possibly old, possibly corrupt) assembly that already exists.
Bruno de Medeiros
May 09 2018 14:00
Hi, I am doing and assembly with a reference genome and I noticed in a test with a small part of my data that the final vcf file provides coordinates to ipyrad loci, not the original reference. Is there any file that I can access with a mapping of ipyrad final loci to the reference genome?
Veronica Reyes
May 09 2018 20:03
Hi, I have a question about restriction overhang. The example is (e.g., C|TGCAG -> TGCAG) : but if I have MspI (C|CGG -> CGG) I should use CGG in params?
or is CCG?