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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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AttributeError: ('PyRanges object has no attribute', 'regionID') with create_cistopic_object_from_fragments #316

Closed SITRR closed 3 months ago

SITRR commented 3 months ago

Hi!

I'm having an issue that was previously described in 146. When running the create_cistopic_object_from_fragments with my dataset, I encounter the error AttributeError: ('PyRanges object has no attribute', 'regionID'). @SeppeDeWinter suggested using pandas version 1.5, which I am using but still encountering the same error.

It's apparent that some of my samples don't pass the QC thresholds based on a FRIP cutoff of 0.4 (I've attached the QC plots). Could these samples be causing the problem? Thanks!

combined_qc.pdf

SeppeDeWinter commented 3 months ago

Hi @SITRR

Indeed, if you are retaining not a single barcode from these samples this could cause the issue you are facing.

If you want to exclude these samples entirely from the analysis I would suggest to remove them from the fragment_dict variable.

All the best,

Seppe

SITRR commented 3 months ago

@SeppeDeWinter Thank you for getting back to me :) I've excluded those samples and it now runs smoothly!