Hi,
I have ran IgDiscover on a dataset of Rhesus Macaque IgM sequences. The final/database/V.fasta file appears to have only 2 sequences. How can I generate a fasta file with all of the V genes that this sample has?
I can’t speak to IgDiscover (although the developers will likely chime in here), but partis has a similar germline inference functionality. Note that if you’re on non-human species you’ll want to indicate that with --species (see here). The full inferred germline will be in a fasta file in the parameter dir (see previous link for full path details), and new alleles can also be written separately with –new-allele-fname.
Does partis annotate receptor isotype?
No, it only focuses on the vdj part. It actually (by default at least, you can change this with –dont-remove-framework-insertions) trims off the constant regions and then collapses sequences with identical vdj regions. If I needed isotype I’d get that with igdiscover or something and merge that info with partis output in a separate step.