how does isoquant deal with same cellular barcode across replicate files?

[sparthib]

Hi there,

for single cell bam files that I am processing in the same isoquant command, how does Isoquant deal with cellular barcode found across multiple bam files? Does it aggregate this information across bams into the final counts matrix or does it keep information from just one of the bams?

Thanks,
Sowmya

[andrewprzh]

Dear @sparthib

Yes, all reads having identical read group (i.e. barcode) will be aggregated together independently of whether they are in the same BAM or distinct.

Best
Andrey