How are barcodes identified in kallisto bustools

[Adam Woolfe]

Hi,

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.

thanks!

Adam  

[Pall Melsted]

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

--
You received this message because you are subscribed to the Google Groups "kallisto and applications" group.
To unsubscribe from this group and stop receiving emails from it, send an email to kallisto-and-appli...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/kallisto-and-applications/17655eb3-d2e0-47e9-b0e3-49e3a08802f7n%40googlegroups.com.