suwonglab / couplednmf Goto Github PK

So I am trying to run this tool and I've fiddled around with changing / ensuring the format of the input is correct - I'm not quite sure where I am going wrong here. Any help would be appreciated.

[in]:
python coupleNMF.py -k 9 -E rna_matrix.txt -PeakO atac_matrix.txt -E_symbol ../sample_RNA_count/outs/filtered_feature_bc_matrix/features.tsv.gz -P_symbol ../atac_outs/filtered_peak_bc_matrix/peaks.bed -pe ../common_data/RE_gene_corr_hg38.bed -lambda1 0.04 -lambda2 25

[out]:

Loading data...
Traceback (most recent call last):
  File "coupleNMF.py", line 67, in <module>
    pindex = P_symbol.index(data[0])
ValueError: 'chr1' is not in list

Hi!
I have a sample (no labeling) of stem cell differentiation data in both scRNA-seq and scATAC-seq, but I only have one BAM file from 10x. Just wanna make sure that your method could be applied to my data, coz I want to get combined clustering result.
Thank you for your help!