Can spl-IsoQuant be used for 10x visium+ONT data?

[xyz202310]

Hi,
Thanks for your great work! Can spl-IsoQuant be used for the data combined by 10x visium and ONT? Thank you!

[andrewprzh]

Dear @xyz202310

Thanks for the feedback!

If you imply the older version of 10x Visium (not HD), then as far as I recall it has the same molecules structure as 10x single-cell 3' v3 (R1 - 16 bp barcode - 12 bp UMI - polyT - cDNA). If so, then you can simply run spl-IsoQuant with --mode tenX.

Let me know if you have any troubles, I haven't used that mode for a while.

Best
Andrey

[andrewprzh]

@xyz202310

New Spl-IsoQuant 2.1 supports Visium 3' and Visium HD protocols.

[xyz202310]

Great, thanks! I'll give it a try.