Comments (2)
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.
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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from gotcha.