search

aertslab / pycistarget

pycistarget is a python module to perform motif enrichment analysis in sets of regions with different tools and identify high confidence TF cistromes.
Other
13 stars 4 forks source link

run_pycistarget #24

Open zhangqc723 opened 1 year ago

zhangqc723 commented 1 year ago

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

zhangqc723 commented 1 year ago

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

SeppeDeWinter commented 1 year ago

@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 commented 1 year ago

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

SeppeDeWinter commented 1 year ago

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