Using velocyto on 3'UTR 10x single-cell RNA-Seq data

Question

[Sergio]

Hello,

I have a naive question about using Velocyto on 3' single-cell data.

My doubt is about the minimal read length that is required to obtain useful information from the data: Velocyto relies on spliced and unspliced reads ratio, and I am afraid that single-end reads, if too short, would not be enough for obtaining this information and consequently the RNA velocity.

Do you have any kind of suggestions or experience on that?

Thanks a lot.

Answer 1

[ATpoint]

Just run it. Off-target of the reverse transcription primer will capture lots of unspliced reads during livrary prep. That's how everyone does it. Just do.

[Sergio]

Yes, I'll try it. Thanks for your feedback