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During our colab, the Smed annotation did not have start and stop codons annotated which was causing issues. My hypothesis is therefore that there is something wrong/missing with your new...

If we ever move over to pyproject.toml, we could replace versioneer with [versioningit](https://github.com/jwodder/versioningit), a package we don't have to install.

That's a weird one! No clue why it's working with one, but not the other... We're attempting to upgrade gimme on bioconda now, and I secretly hope that might fix...

I thought I'd pack it up since you've already wrote the whole solution, but I understand this implementation might not be desired. Unfortunately, I have no idea how to implement...

Thank you for the insight! I've run this with two tutorials and two browsers and it seems to be performing well enough on both Chrome and Firefox (I'll ask my...

No idea what the error is! I'll post the code that worked for us below. We tested this on Rstudio and Rstudio Server. ``` ```{js print2pdf1, context="server"} // the following...

On a different server, with way more threads, and with the `--peek-guess` flag it did run. Tomorrow I'll restart lima on my machine with the flag to see if it...

It appears to be related to the specific bam file. After processing the public ccs file using `skera`, `lima` worked just fine. Perhaps the sread file I had downloaded was...

Salmon can accept FASTQ files in [mapping-based mode](https://salmon.readthedocs.io/en/latest/salmon.html#quantifying-in-mapping-based-mode), or BAM files in [alignment-based mode](https://salmon.readthedocs.io/en/latest/salmon.html#quantifying-in-alignment-based-mode). Seq2science has only implemented the mapping based mode. If your are using Salmon for gene quantification,...

If you wish to create BAM files with STAR, and them feed them into Salmon, there are some considerations: 1) Why do you wish to do this in the first...