brie-count smartseq3 bam

[lishuangshuang0616]

Hello,
I would like to ask how to analyze smartseq3 data in brie2, and how to set --UMItag in brie-count to obtain umi reads and internal reads at the same time.

brie-count -a AS_events/SE.lenient.gtf.gz -s test.filtered.Aligned.GeneTagged.UBcorrected.sorted.bam -o output --cellTAG BC --UMItag UB --nproc 50 -b cell_barcode_filter.tsv

[huangyh09]

Thanks for the question. We haven't tried smart-seq3 data. Feel free to contribute to this repo to support this type of data.

Yuanhua