Hey everyone, inside parameters for MISO: https://nf-co.re/rnasplice/1.0.4/parameters/#miso, in "--miso_genes," the default's

ENSG00000004961, ENSG00000005302

. I was able to use that for Homo Sapiens good. But for mouse, Mus musculus, because their gene ID is in this format:

ENSMUSG000...

, any idea what could be the good "default" for Mus musculus (mouse) species be?

You can use the ID(s) for any gene(s) that you are interested in (provided it is in the GTF). It would be good if those genes show at least some expression, otherwise there is not much to see. If you want to use the orthologs for the human defaults,

ENSMUSG00000031352

(Hccs) is the ortholog of

ENSG00000004961

(HCCS), whereas

ENSG00000005302

(MSL3) has two orthologs --

ENSMUSG00000031358

(Msl3) and

ENSMUSG00000047669

(Msl3l2).

Hi Thomas Danhorn, I hope you're doing well. I have a question similar to Michael's, but I would like to know if you have any suggestions on where I can find a file with the known AS (Alternative Splicing) data in mice. Do you have any ideas or resources that could help? Thank you for your time and assistance!

Transcripts for genes are usually annotated in GTF (or GFF3) files. From those you can see splice junctions and deduce alternate events. Those are available from a variety of sources, e.g. NCBI, Ensembl, Gencode, or UCSC. I personally like Ensembl, they have unambiguous IDs, get updated regularly, and have "releases" (versions) so you know exactly what you used for reproducibility. Here is the newest version (release 113) of a mouse GTF. This one goes with the GRCm39 assembly, if you want GRCm38, you will have to use release 102.