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List of valid cellular barcodes

Posted By: rory, on Aug 4, 2017 at 11:29 AM

Hello,

 

Is there a place we can go to find a list of valid cellular barcodes for the Chromium v3 setup? I poked around on the website but couldn't find it anywhere. Thanks!

11 Replies

Re: List of valid cellular barcodes

Posted By: pnpiano, on Aug 7, 2017 at 6:31 AM

Hi Rory,

 

I am not exactly sure about a list of barcodes readily available. From what I've been told, the barcodes are produced randomly and then tagged to each read somehow. However, I am also looking for a way to get this list of barcodes as it would ease the process of demultiplexing the reads of the dataset I am working with.

Re: List of valid cellular barcodes

Posted By: shauna-10x, on Aug 7, 2017 at 1:40 PM

Hi,

 

Thanks for posting on the 10x Community!

 

I spoke with our support team and you can find the whitelist of barcodes in a text file in the Cell Ranger software.  Here's the path to find the file: cellranger-2.0.0/cellranger-cs/2.0.0/tenkit/lib/python/tenkit/barcodes/737K-august-2016.txt.

 

Best,

Shauna

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Re: List of valid cellular barcodes

Posted By: rory, on Aug 7, 2017 at 1:52 PM

Hi Shauna,

 

Thanks for following up! What is the difference between the 4M-with-alts-february-2016.txt and 737K-august-2016.txt? It looks like 4M-with-alts-february-2016.txt is a superset of 737K-august-2016.txt, but the 4M with alts has 6.5x more barcodes in it. Where are the extra barcodes from? Thank you!

Re: List of valid cellular barcodes

Posted By: shauna-10x, on Aug 7, 2017 at 4:34 PM

I'm following up with support and will get back to you as soon as possible.  Thanks!