Jason Stajich

hi - the species flag for protein annotation doesn't matter. The annotate step is only matching proteins it isn't running augustus anymore - that only happens with `predict` step and...

to answer the first question in `predict` 1. `--busco_seed_species botrytis_cinerea` -- this is what augustus starting species to use when running the [BUSCO](https://busco.ezlab.org/busco_userguide.html#command-line-options) runs. BUSCO can start with default parameter...

Did you run the update step with rnaseq? That is only way alt splicing is incorporated based on evidence.

PeterKennedy showed those early ONT results at MSA22 that you had worked on @nextgenusfs - def limited value for the older amplicons, but we also discussed with others doing PacBio...

You probably want to merge this into a python3 branch rather than master/main until you are ready to do a release for python3?

But this should help solve #2

I believe `protein2genome` is incorporates the model with intron states while `protein2dna` is more about only modeling frameshifts in a protein to DNA alignment. https://github.com/nathanweeks/exonerate/blob/master/doc/man/man1/exonerate.1 ``` protein2dna This model compares...

A pull request via git would make it easiest to incorporate your changes. If not I expect someone can make these fixes.

Thanks that does fix the error, however bigwig or bam tracks are not rendered in the resulting SVG file.

Okay. Glad it worked. Since this is just a deposit for my working scripts I don’t have unit tests for these but originally I did have test cases this was...