How are barcodes identified in kallisto bustools

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Adam Woolfe

Sep 13, 2022, 8:15:17 AM9/13/22
to kallisto and applications
I am using an in-house barcoding system that is not one of the barcode systems when using '--list'. There is a 10bp barcode, following by a 6bp UMI. I point the program to the whitelist file of barcodes too.  

I therefore use the -x option 0,0,10:0,10,16:1,0,0

Can someone tell me how the barcodes are identified? Does it require a perfect match to a whitelist barcode or does it allow a single mismatch for example? Given the rate of mutations introduced by cDNA, PCR and sequencing , if it is perfect match there will be a certain proportion of reads that will be missed by a perfect match approach.



Pall Melsted

Sep 30, 2022, 1:52:47 PM9/30/22
to kallisto and applications
kallisto writes the barcode as-is to the BUS file

bustools has a correct subcommand that can do the single bp mismatch correction against a whitelist. If no whitelist is available the whitelist subcommand can generate a sample-specific one. 

- Pall

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