Error when running brie-count: IndexError: list index out of range

[fweberling]

Hi,

I run brie-count on a .bam file and use the provided SE.gold.gtf annotation. Unfortunately, I receive this error message:

What is the reason for it? I used this code in the command line:

brie-count -a $path2gtf/SE.gold.gff3\ -s $path2bam/Aligned.sortedByCoord.out.bam\ -b $path2barcodes/barcodes.tsv.gz \ -o $path2out/brieCount \ -p 15

I would appreciate some feedback!

Cheers,
Friedrich

[huangyh09]

Hi Friedrich,

Thanks for reporting the issue. Can you double-check if the cell barcode is used in the bam file? The format generally has a suffix of "-1", e.g., GTGCC*-1. Therefore, if no cells are matched, it will return zero cells in the matrix and raise the error.

Best
Yuanhua