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aertslab / scenicplus

SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.
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multi_ome_mode = False #372

Closed orian116 closed 5 months ago

orian116 commented 5 months ago

Hello,

Thank you for the updates o the package. I am running scenic+ using snakemake from sceniplus '1.0a1'. When I get to the "localrule prepare_GEX_ACC_multiome:" step I get the following error: " No cells found which are present in both assays, check input and consider using bc_transform_func!"

In my scATAC and scRNA datasets, I don't have the same barcodes but I have the same cell types annotated between the two. I know in the old version of scenic+ there was a way to create a pseudo multiome dataset simply by passing multi_ome_mode = False. Is there a way to do it automatically in this version? I see the bc_transform_func in the config.yaml but what function/argument do I pass to it?

jesswhitts commented 5 months ago

You want to edit the Snakemake config.yaml file, under 'params_data_preparation:' change 'is_multiome: False' and also set 'key_to_group_by:' to the name of your common cell type field

Best, Jess (not a part of scenic+ dev team btw, just passing...)

orian116 commented 5 months ago

Thank you that worked! I just had to play around with memory and nodes on my cluster.

SeppeDeWinter commented 5 months ago

Thank you for answering @jesswhitts, that's indeed correct!

Good luck with the analysis @orian116

Best,

Seppe