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Re: List of valid cellular barcodes

Posted By: jens-10x, on Aug 7, 2017 at 11:05 PM

Hi Rory,

 

The 4M-with-alts-february-2016.txt is the barcode whitelist for our Genome application. For the Genome assay we load ~4 million different barcoded Gel Beads. This is different to our Single Cell assay which only uses  ~750k barcoded Gel Beads as input.

 

The barcode whitelist for the Genome application is located here:
longranger-2.1.3/longranger-cs/2.1.3/tenkit/lib/python/tenkit/barcodes/4M-with-alts-february-2016.txt

 

Best,

Jens

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Re: List of valid cellular barcodes

Posted By: rory, on Aug 9, 2017 at 12:15 PM

Thank you! That is super helpful.

Re: List of valid cellular barcodes

Posted By: mibrahim, on Mar 18, 2019 at 3:40 AM

Hi

 

I was wondering if this list of valid cell barcodes is still the same one for scRNA-Seq solution version 3? or has the list been expanded?

 

thank you

 

best wishes

Mahmoud

Re: List of valid cellular barcodes

Posted By: juan-du, on Mar 19, 2019 at 10:16 AM

Hi Mahmoud,

 

We introduced a new barcode whitelist for Single Cell 3' v3 chemistry solution.

 

You can find the barcode whitelist file bundled inside your Cell Ranger v3 installation, e.g. 

cellranger-3.0.2/cellranger-cs/3.0.2/lib/python/cellranger/barcodes/3M-february-2018.txt

 

Best Wishes,

Juan

 

Juan Du, Ph.D.

Software Field Operations Engineer

support@10xgenomics.com