How to find common alternative splicing events or novel transcripts among different batches of samples?

Question

[wenhui]

Hello,

Recently, I am interested in finding common mutation among different batches of samples. But I have not found approaches to determine common alternative splicing and novel transcripts. Any advice about this topic is appreciated. Thank you.

Answer 1

[Kevin Blighe]

I believe that the HISAT2 / StringTie pipeline is suited for this. This was originally TopHat2 / Cufflinks.

• The publication: Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown
• HISAT2 download
• StringTie download

Answer 2

[Kristoffer Vitting-Seerup]

The pipeline Kevin suggest will give you the basis for doing the downstream analysis of acutal splice events.

If you are interested in isoform switches (which enables easy biological interpretation) you can use one of my tool IsoformSwitchAnalyzeR. Alternatively rMATS or DEXSeq can be used to find exon-level differences. Leafcutter lies somewhere in between analyzing clusters of splicing.

[Kevin Blighe]

The pipeline Kevin suggest will give you the basis for doing the downstream analysis of acutal splice events.

Thanks Kristoffer, that is certainly true, and I also recommend the programs that you have mentioned.