Question: What is a barcode whitelist?
Answer: A barcode whitelist is the list of all known barcode sequences that have been included in the assay kit and are available during library preparation.
For example, there are roughly 737,000 cell barcodes in the whitelist for Single Cell 3' Gene Expression (v2 chemistry), 5' Gene Expression, and V(D)J applications. Here are the first 10 lines of the corresponding barcode whitelist 737K-august-2016.txt:
AAACCTGAGAAACCAT AAACCTGAGAAACCGC AAACCTGAGAAACCTA AAACCTGAGAAACGAG AAACCTGAGAAACGCC AAACCTGAGAAAGTGG AAACCTGAGAACAACT AAACCTGAGAACAATC AAACCTGAGAACTCGG AAACCTGAGAACTGTA
You can find the barcode whitelist files bundled inside your Cell Ranger installation:
- Cell Ranger 4 and later:
cellranger-x.y.z/lib/python/cellranger/barcodes/ - Cell Ranger 3 and earlier:
cellranger-x.y.z/cellranger-cs/x.y.z/lib/python/cellranger/barcodes/