Question regarding transcript quantification with hybrid seq

Question

[shinyjj]

Hi all,

Is there any hybrid seq tool for transcript quantification? Technically, wouldn't hybrid seq be a better tool than just long read as short read can increase quantification as it has more coverage?

Or would using both long and short read in different proportions be heavily skewed in favor of a much higher contribution from long-read and additional short read information make the results worse?

I am not sure if salmon can work with hybrid seq? I wonder what people think.

[GenoMax]

Answers from @Rob Patro author of salmon:

long read + salmon? (transcript abundance)
salmon with long reads

Note: I now see that one of the threads above is your own where @Rob had responded.

Practically library prep needed for short and long reads is quite different. So it would be difficult to sample in an equivalent manner from any experiment. If one has the funds available then one could try doing an experiment with both technologies at the same time.

[jared.andrews07]

Some groups here tend to use Iso-seq or such to generate accurate assemblies (especially for lncRNAs) coupled with short-read for quantification.