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Cell barcode and UMI with linked-reads

Posted By: dridk, on Mar 5, 2019 at 6:12 AM

Hi,

 

With linked reads experiment, I cannot figure out the difference between barcode and UMI.

 

- 10x barcode = cell barcode ( unique to gem ) + UMI ( unique to molecule )  ?

- 10x barcode = cell barcode only ( unique to gem )?

5 Replies

Re: Cell barcode and UMI with linked-reads

Posted By: Mike_at_10X, on Mar 5, 2019 at 9:59 AM

Hello,

 

The linked read libraries are a little differnt than that gene expession libraries. The linked read libraries do not contain a UMI. The barcode is the firtst 16bp of read one. Page three of this doc shows a cartoon of the final library. https://assets.ctfassets.net/an68im79xiti/1Jw6vQfW1GOGuO0AsS2gM8/61866afe8c8af5e0eecf6a3d890f58aa/CG...

 

the individual molecules that made it into each gem are inffered bioinformaticaly by the Long Ranger pipleine described on our support site here: https://support.10xgenomics.com/genome-exome/software/pipelines/latest/what-is-long-ranger

 

I hope this is helpful. If you have more questions feel free to send us an email at support@10xgenomics.com

 

Best,

Mike

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Re: Cell barcode and UMI with linked-reads

Posted By: dridk, on Mar 5, 2019 at 10:13 AM

Thanks ! it's is clearer now !

Could you confirm those 16 mers barcodes  are defined inside a  "whitelist" file somewhere ?

 

 

 

 

Re: Cell barcode and UMI with linked-reads

Posted By: Mike_at_10X, on Mar 5, 2019 at 10:42 AM

Yep. The whitelist is bundled with Long Ranger. Here:

longranger-2.2.2/longranger-cs/2.2.2/tenkit/lib/python/tenkit/barcodes/4M-with-alts-february-2016.txt

Re: Cell barcode and UMI with linked-reads

Posted By: dridk, on Mar 5, 2019 at 11:38 AM

Ok ! thanks ! Smiley Happy

 

And the goal of longranger mkfastq compared to bcl2fastq is to trim those barcodes ?

Does it add the barcode information somewhere in the fastq header ?