best method for splicing variant analysis if I have the counts already?

Question

[decppced]

Hello everybody.

I am new in coding and RNA-analysis, so please bear with me. I am trying to find some package (and pipeline if possible) to run an analysis to find the differentially expressed isoforms between my conditions. I already have the counts of all the isoforms and the annotations. What is the best tool for this?

I have found that EdgeR can deal with splicing variants but it needs the sequence and exons; but as I said, I already have the isoform counts so I don't need to go back in steps. Any idea?

Thanks

Answer 1

[ashish]

You can try DRIMSeq for differential transcript usage. If you can get hold of the raw data and restart the analysis QoRTs -> JunctionSeq is the way to go.

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Can DRIMSeq handle the already counted isoforms? Thanks

[ashish]

Yes it can, check out the vignette

[decppced]

Awesome, thanks so much!

Answer 2

[Istvan Albert]

If you already have the counts isoforms why would you need exon information?

Typically you would need the splicing information (junctions/exons) to be able to assign counts to an isoform. But if you already have the information you can move onto the statistical analysis. The statistical analysis does not need the splicing information.

[decppced]

you are right, that is what I am saying, I have all that and I don't want to go back to that using packages that ask me to work with raw data. I want something that can deal with the counts of the isoforms which is what I have right now. I hope I made myself clear this time. Any suggestions? thanks again