Jason Stajich

funannotate can only predict multiple isoforms if you run with RNAseq and do the [`update`](https://funannotate.readthedocs.io/en/latest/update.html) step with RNAseq to allow PASA to predict isoforms

PTCHD1_1 is about gene "functional" assignment but MBRI001 is the gene locus name - take a look at your GFF file and you can see gene location info - isoforms...

>While I still am hoping to get a file that is uniform with NCBI format I'm gathering that perhaps submitting these to NCBI with the funannotate output will generate the...

>Perhaps a better question to ask here is why I might see excessive species specific orthogroups? - It depends on how close your comparison species are. - Are you masking...

patches always welcome - we also put more cleaning stuff in AAFTF https://github.com/stajichlab/AAFTF/issues/7 - one issue I saw was at leats in the version NCBI had at beginning requires huge...

oh that would be better - yeah that would be good to add in - just I think @nextgenusfs was thinking of separating assembly cleaning from annotation but let's see...

My thoughts exactly. I agree this is best thing to do. On Tue, Aug 9, 2022 at 2:39 PM Jon Palmer ***@***.***> wrote: > For reference, we could integrate our...

I def have this bug too- I have not worked on the workaround - but if you want to provide the option to run v1 or v2 that would be...

Is this a funannotate question? Where did the CDS files come from that you used for the selection analysis? Are you doing pairwise or multi-species analysis? You can check your...

where did your genbank files come from - I now there are some parsing challenges at times - but are these annotations you perhaps did with funannotate?