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What is a barcode inclusion list (formerly barcode whitelist)?

Question: What is a barcode inclusion list?

Answer: A barcode inclusion list 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 inclusion list for 5' v2 chemistry. Here are the first 10 lines of the corresponding barcode inclusion list 737K-august-2016.txt:

AAACCTGAGAAACCAT
AAACCTGAGAAACCGC
AAACCTGAGAAACCTA
AAACCTGAGAAACGAG
AAACCTGAGAAACGCC
AAACCTGAGAAAGTGG
AAACCTGAGAACAACT
AAACCTGAGAACAATC
AAACCTGAGAACTCGG
AAACCTGAGAACTGTA

You can find the barcode inclusion list 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
(Cell Ranger v8.0 and v8.0.1)
3M-3pgex-may-2023_TRU.txt.gz*
(Cell Ranger v9.0 and later)

 Single Cell 3' v4
3M-febrary-2018.txt.gz
(Cell Ranger v8.0 and older)
3M-february-2018_TRU.txt.gz*
(Cell Ranger v9.0 and later)		 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)

*Reasons for the revised inclusion list names can be found in this article.


Products: Single Cell Gene Expression, Single Cell Multiome ATAC + Gene Expression, Single Cell ATAC

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Last edited: Feb 2025