RNA-Seq Cell Barcode Whitelist 10X

Question

[kanwarjag]

I am trying to get RNA-Seq Cell Barcode Whitelist for version 3 RNAseq of 10X. Is it a standard file Does any one know source of tis file outside cell ranger.

[mathieu.bahin]

Hi,

I have a related question. I just ran cellranger and alevin on a 10X dataset downloaded on GEO (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM4284237) that says: "10X Genomics Chromium 3' v2 kit according to manufacturer's protocol".

For both softs, the overlap between found barcodes and 3M or 737k lists are ridiculously small. Are there other lists somewhere? Is there something I misunderstood?

Cheers, Mathieu

[GenoMax]

Use the 737K list for v.2 of the kit. See this link.

[mathieu.bahin]

Thanks, there is a 100% overlap! :) I previously used a "jag" list of BCs, I thought it was the same...

Answer 1

[ATpoint]

If you mean by outside that you do not want to download the entire package then you can directly download it from the GitHub version of CellRanger:

https://github.com/10XGenomics/cellranger/raw/master/lib/python/cellranger/barcodes/3M-february-2018.txt.gz