multiple 10x samples integration to run brie-count

[TuoCai2000]

Dear Yuanhua, Thank you for developing BRIE! Now I have eight samples which have sequenced by 10x genomics, so I get 8 bamfiles and 8 barcodes.tsv.gz. In your introduction for BRIE2, you give an example like: brie-count -a AS_events/SE.gold.gtf -s possorted.bam -b barcodes.tsv.gz -o out_dir -p 15,so I wonder if there is a way I can input eight bamfiles and their 8 different barcodes.tsv.gz in one command line, so that I can get one h5ad file result instead of eight h5ad files? If I can't, can you give me a suggestion for integrating eight h5ad results? My integration isn't ideal. I am looking forward to your apply, thank you so much!

Tuo

[huangyh09]

Hi Tuo,

Thanks for reporting the issue. BRIE2 doesn't support multiple 10x bam files, but it is relatively straightforward to combine all h5ad files (with scanpy / anndata), as they all have the same list of splicing events. You may need to add a sample suffix to the cell barcodes to each h5ad file so that cells with identical barcodes from two samples won't be combined.

Yuanhua