Help with bc_transform_func for GEX job in Snakemake

[ptk1601]

Hello!

I am trying to fix a discrepancy between my barcodes in my GEX and ATAC data. My GEX data barcodes' format is currently as follows: stat3ff_AAACAGCCATTGACAT-1 and my ATAC data barcodes looks like: AAACAGCCATTGACAT-1_stat3ff. What is a lambda function for bc_transform_func I can use to adjust this? Unfortunately when I try to split by underscores, it seems that SCENIC+/Python isn't recognizing it?

[ptk1601]

I've fixed this issue just by changing the format of the cell_names part of the cistopic_obj, but I am now getting this error. Is there anything I can do to fix this?

File "/gpfs/gsfs12/users/kimpt/conda/envs/scenicplus/lib/python3.11/site-packages/pandas/core/indexes/base.py", line 6168, in _raise_if_missing
raise KeyError(f"None of [{key}] are in the [{axis_name}]")
KeyError: "None of [Index(['CACATTAAGTTCCTGC-1', 'TCATTACTCTCACAAA-1', 'TTAGCAATCACACAGT-1',\n 'TTGGGTTAGCTTCTCA-1', 'TCTTGTCCAAAGCTCC-1', 'CTAAATGTCATGCGTG-1',\n 'TGAGGTGCATAAAGCA-1', 'GACATAGAGACAACGA-1', 'TAATGGACACCGGCTA-1',\n 'GGGTTATTCGGTTTCC-1',\n ...\n 'CTAATCCGTATACTGG-1', 'GCCTACTTCCCTGGAA-1', 'CCCGCAACAACACCTA-1',\n 'ACAGTATGTTTGGTTC-1', 'AATCATCCAAGCTTTG-1', 'ATGAGCCGTGGATTGC-1',\n 'AGGTCAAAGATGGAGC-1', 'TGCCATTGTGTGCAAC-1', 'TTATAGCCATACCCGG-1',\n 'CTAATAGTCCCAGTAG-1'],\n dtype='object', length=18273)] are in the [columns]"

I did get a message recommending to call .obs_names_make_unique, so does this have any effect on this error?

[sheyiphunmi]

Have you considered formatting the cell_names(indices) in your GEX object instead of the cistopic_obj?

NOTE:
I am not a part of the scenic+ team; I am just a user who reads some of the issues.

[ptk1601]

Have you considered formatting the cell_names(indices) in your GEX object instead of the cistopic_obj?

NOTE: I am not a part of the scenic+ team; I am just a user who reads some of the issues.

Hi! Thank you so much for the suggestion. I am now working with the GEX object. I have copied the cell barcodes to a column in the GEX object, but yet it seems that SCENIC+ cannot find/detect them...

[sheyiphunmi]

The problem might be more than copying the barcodes to a new column because this doesn't change the row index or names of your metadata and GEX count matrix.

For instance, the index of your metadata (adata_atac.obs) will not be changed. Do you have a Seurat or SCE version of this data? If yes, I suggest formatting the row names of your count matrix before converting to an "h5ad" object.