Good morning everyone, someone has results using mouse genomes?? can you shared yur experiences with me, thank you

I haven't used it with mouse, but it should work the same way as with human (or anything else with multiple annotated transcripts). You can give the pipeline any genome FASTA and GTF (and STAR index, if you have one). There are certain tools that will rely on annotations in the GTF, so those will work as well as the GTF permits (if it is incomplete, you'll get suboptimal results), but I would think mouse should be OK.

Thank you Thomas for your response, I was working before with it, but it has a problem with some R packages, that do not acept duplicated names, which annotation do you used in human?

I use Ensembl whenever I can. I like that they have an internally consistent system of IDs and they have "releases", so if you pick one (I think 114 is current) and stick to it, everything should be compatible. Note that the "main" mouse genome (GRCm38/39, mm38/39) is based on the C57BL/6 strain. I think the most basic genes should be similar in all mouse strains, so you can get away with using that, but if you have a different strain and want to be "accurate", you would have to find an alternate genome assembly and the matching gene annotation (GTF). I have never done that, though, so I have no special advice for that. Ensembl might have such files, but I have not looked.

thank you I will try that