Hi, I am using run_pycistarget for zebrafish analysis, I am wondering which species name should I use? I tried species = 'danio_rerio'; or species = 'drerio', but none of the names work.

[ljljolinq1010]

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[SeppeDeWinter]

Hi @ljljolinq1010

I transferred your issue to the discussions because it's more a question and not a bug.

When you say it does not work I guess you're getting the following error message?

Unable to load annotation for danio_rerio

The reason for this is that we don't provide motif-to-TF annotations for zebrafish at this moment (we only have human, fly and mouse). You can generate your own custom annotation based on our annotations (for example based on orthology).

Once you've done this you can provide this custom annotation using the parameter path_to_motif_annotations.

I hope this clarifies things.

Best,

Seppe

[ljljolinq1010]

I see, thanks a lot for your quick and informative reply. very cool method.

[mtrebelo]

Hi @ @ljljolinq1010

I am also running SCENIC+ with zebrafish data (danRer11). Which data did you use for the rankings_db, scores_db and motif_annotation at the 'Cistarget databases' point of the tutorial?

Thanks a lot in advance.