run_pycistarget

[zhangqc723]

Does run_pycistarget only ueed for homo_sapiens, mus_musculus, drosophila_melanogaster and gallus_gallus? I notice this Parameters--species only contain this four species?

[zhangqc723]

How to do if I want to run it for Rat?

[SeppeDeWinter]

@zhangqc723

You can also use pycistarget for Rat. The only thing is we don't provide motif-to-TF annotations for species other than mouse, human, fruit fly and chicken.

You can try to generate this annotation yourself based on orthology (for example from mouse to Rat).

Best,

Seppe

[zhangqc723]

Thanks for your response! And How to set the parameters --species when I run run_pycistarget?

[SeppeDeWinter]

Hi @zhangqc723

You can set it to 'custom' besides that you should also provide your own gene annotation file using the custom_annot parameter.

Best,

Seppe