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