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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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'PyRanges object has no attribute', 'Count' #437

Closed laki-spk closed 2 months ago

laki-spk commented 2 months ago

Hi @SeppeDeWinter and team

This is a great tool and thank you for establishing this. I've been using this with several data types and I'd no issue before. But now I am running it with Human data set, and it is working up to the MAC2 calling step.

But I can't move fast the following script and I am getting the following error;


> from pycisTopic.iterative_peak_calling import get_consensus_peaks
> # Other param
> peak_half_width = 250
> path_to_blacklist= '/temp_work/ch250798/Scenic/pycisTopic/blacklist/hg38-blacklist.v2.bed'
> # Get consensus peaks
> 
> narrow_peaks_dict = pickle.load(open(os.path.join(work_dir, 'scATACkk/consensus_peak_calling/MACS/narrow_peaks_dict.pkl'), 'rb')) 
> consensus_peaks=get_consensus_peaks(narrow_peaks_dict, peak_half_width, chromsizes=chromsizes, path_to_blacklist=path_to_blacklist)

image

Could you please help me troubleshoot this issue?

Thank you

laki-spk commented 2 months ago

Never mind I was able to resolve it.