Cistopic object with NaN for a lot of criteria

[tu4n-p]

Hi there, I'm analyzing Dmel scATACseq for embrogenesis with pycistopic. Things went well until I checked cistopic object and all of the Log_total_nr_frag | Log_unique_nr_frag | Total_nr_frag | Unique_nr_frag | Dupl_nr_frag | Dupl_rate | Total_nr_frag_in_regions | Unique_nr_frag_in_regions | FRIP | TSS_enrichment were NaN for all rows.
I was wondering if there could possibly anything that I can work around this? Thank you,

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[cbravo93]

Hi @tu4n-p !

How did you initialize the cistopic object? Did you add the cell data externally (add_cell_data)? Can you show the barcode names? Can you check rowsums for those barcode? Can you provide the full code?

C

[tu4n-p]

So I followed Single_sample_workflow where I started out with annotated ATAC fragments from my lab (we don't have co-assayed RNA seq). When I did quality control, I was able to plot out TSS and FRiP

but when I added cell_meta using cistopic_obj.add_cell_data(cell_data, split_pattern='-') , I ran into the NaN problem.
This is the code I used to create cistopic obj:

This is the cell_data I used

One barcode row:

[cbravo93]

Sorry for the lay response @tu4n-p ! You have to add -10x_multiome_brain to the index names in the metadata.

C

[yojetsharma]

Were you able to solve this?