Question: For the Multiome ATAC + Gene Expression product, the 10x Barcode sequences on the ATAC and GEX specific primers on the same Gel Bead are not identical. How does Cell Ranger ARC translate between the two sets of barcodes?
Answer: Indeed, the ATAC and GEX primers for the same cell contain different 10x Barcode sequences, as explained on this page. Cell Ranger ARC handles barcode translation behind the scene so that ATAC and GEX data from the same cell are properly associated.
Once Cell Ranger ARC is installed, it contains two separate lists of allowed barcodes:
- ATAC barcode: <path_to_cellrangerarc>/cellranger-arc-1.0.0/lib/python/atac/barcodes
- GEX barcode: <path_to_cellrangerarc>/cellranger-arc-1.0.0/lib/python/cellranger/barcodes
The two sets of barcodes are associated by line number. For example, the barcode from line 1,748 of the GEX barcode list is associated with the barcode from line 1,748 of the ATAC barcode list.
For the raw and filtered feature-barcode matrices that is produced by Cell Ranger ARC, all the barcodes are translated to the corresponding entry on the GEX barcode list.