Question about support for 10X 5' kit version 1 and utilization of barcodes form short-read

[Kyung-TaeLee]

Hi, thank you for the amazing tool and constant updates.

I have single-cell Nanopore sequencing data from 10X 5' kit version 1 and 1.1 so I am wondering if BLAZE support for this kit for barcode and UMI identification.
And I have single-cell short-read data from same library so Is BLAZE can also utilize list of barcodes from short-read data for better performacne?

Thank you.
Best regards,
KyungTae Lee

[youyupei]

Hi @Kyung-TaeLee, although I haven't tested it, the read structure of 5' v1 seems to be identical to 5' v2 so you could probably run it on a subset of reads with --10x-kit-version 5v2 option.

And yes, you could use list of barcodes from short-read, here is an example:

blaze --no-whitelisting --10x-kit-version 5v2 --known-bc-list <your list of barcode> <input fastq>