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problem with barcode matching about gotcha HOT 2 CLOSED

scZfish avatar scZfish commented on September 17, 2024
problem with barcode matching

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Comments (2)

scZfish avatar scZfish commented on September 17, 2024 1

Thanks. That worked, but since that file is much larger, it ends of taking much more time.

The error I got might be because the barcodes.tsv and singlecell.csv files look different? The .csv file has a header along with count data, while the .tsv file only has the barcode.

I used a join between the outs/singlecell.csv file and filtered_peak_bc_matrix/barcodes.tsv to generate a more restricted singlecell.csv file and then made sure I had the header. This ended up working and much faster than using the full singlecell.csv. If I remove the header, then it threw an error.

In any case, it is working now! Thanks.

from gotcha.

Theob0t avatar Theob0t commented on September 17, 2024

Hi,
Please try using the /outs/singlecell.csv file from the cellranger ATAC output folder as your barcodes.file.path input and see if that fixes the error.
Thanks,

from gotcha.

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