Adding a new organism? (Zebrafish)

[alexwskh]

Hello,

I was wondering if it was possible to add a new species for use with SCEVAN. Our lab studies cancer modeling in zebrafish and I'm quite keen on trying some CNV inferring software. I'm guessing the main thing that needs to be fed in is the GTF annotation?

Any help or suggestions is appreciated, thank you.

[AntonioDeFalco]

Hi @alexwskh,

Thank you for reaching out! Yes, it is definitely possible to add a new species, such as zebrafish, for use with SCEVAN. You’re correct the main requirement is providing a proper GTF annotation.

To achieve this, I need an annotation object similar to EnsDb.Hsapiens.v86 for the human genome. You can create this using the ensembldb package, which allows you to generate an Ensembl-based annotation database for zebrafish (or any other species) by downloading the appropriate GTF file and genome sequence from Ensembl.

If you generate the EnsDb annotation, I’ll make it a priority to add zebrafish genome support to SCEVAN.

Regards.