pyscenic ctx --annotations_fname: how to generate tbl for new species?

aertslab / create_cisTarget_databases

Create cisTarget databases

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pyscenic ctx --annotations_fname: how to generate tbl for new species? #14

Closed mcsimenc closed 2 years ago

mcsimenc commented 2 years ago

Hi, I want to run pySCENIC on a plant species. How can I create a TF annotation file such as motifs-v9-nr.hgnc-m0.001-o0.0.tbl?

mcsimenc commented 2 years ago

I created a table with 0 in the motif_similarity_qvalue and orthologous_identity columns, and "None" in the rest of the "similar" and "orthologous" columns. I put motif info for my target genome in the first 6 columns. To run the pipeline I needed to specify --no_pruning on the command line.