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RNA-Seq Cell Barcode Whitelist 10X

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.

rna-seq
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updated by mathieu.bahin mathieu.bahin • written by kanwarjag kanwarjag

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

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written by mathieu.bahin mathieu.bahin

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

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written by mathieu.bahin mathieu.bahin

1 answer

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

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written by ATpoint ATpoint

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