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 5' v2 chemistry. 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
For more details on the whitelist for 3'v3 chemistry, please see here.
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/
The table below shows which list in the barcodes folder is relevant to which chemistry:
| Name of barcodes list | Chemistry |
| 3M-3pgex-may-2023.txt.gz | Single Cell 3' v4 |
| 3M-febrary-2018.txt.gz | Single Cell 3' v3, Single Cell 3' v3.1, Single Cell 3' HT v3.1 |
| 3M-5pgex-jan-2023.txt.gz | Single Cell 5' v3 |
| 737k-august-2016.txt | Single Cell 3' v2, Single Cell 5' v1 and v2, Single Cell 5' HT v2 |
| 737k-april-2014_rc.txt | Single Cell 3' v1 |
| 737k-arc-v1.txt.gz | Single Cell Multiome (ATAC+GEX) v1 |
| 737-cratac-v1.txt.gz | Single Cell ATAC (located within cellranger-atac installation directory: cellranger-atac-2.1.0/lib/python/atac/barcodes/)
|
| 9K-LT-march-2021.txt.gz | Single Cell 3' LT |
| 737k-fixed-rna-profiling.txt.gz | Fixed RNA Profiling (Present starting from Cell Ranger v7.0) |
Products: Single Cell Gene Expression, Single Cell Multiome ATAC + Gene Expression, Single Cell ATAC
Related KB articles:
Where can I find the barcode whitelist(s) for Single Cell Multiome (ATAC + GEX) product?
Where can I find the barcode whitelist for Single Cell ATAC product?
Barcode translation in Cell Ranger ARC
Last edited: Oct 2023