Salmon and differential splice / exon usage?

[Jonathan Manning]

Does anyone have a recommended protocol for analysing differential splicing with the outputs of Salmon, Kallisto etc? I was looking at Suppa (https://bitbucket.org/regulatorygenomicsupf/suppa), but I don't think it does differential yet. I've been switching to genomic alignment w/ naive counting via DEXSeq, but I'd rather be consistent and use the outputs of Salmon if I could.

Jon

[EDUARDO EYRAS]

Hi Jon,

We have now a version of SUPPA to calculate diff. splicing. 

It works with replicates and it can take any number of conditions with any number of replicates per condition. 

In a couple of weeks it will be available at the repository. Will that be a good timing?

Let me know if you would want to try it earlier. 

Best

Eduardo

[Jonathan Manning]

Hi Eduardo,

Thanks for replying over here, having already done so over at Kallisto. I'm working on a project right now that could use this, so I'll be keen to try it out whenever it's ready. My project's due back to my collaborator in a week or so, so if I could have a look at it soon that would be great.

Jon

[EDUARDO EYRAS]

Hi Jon,

yes, no problem. Please send me an email

eduardo.eyras at upf.edu

We'll try to send you the current code asap

cheers

E.