differential splicing for subset of genes

Question

[Varun Gupta]

Hi Everyone,

I have few RNA-SEQ samples from diseased(8) and normal patients(5). I want to look for my subset of genes(around 80 genes), how does splicing varies in these patients in my subset of genes. I used STAR to align the raw fastq reads.

What software can I use to find whether my subset of genes, differ in splicing in 2 cases;diseased and normal?

Is DEXSeq a good start?

Hope to hear from you

Thanks

Answer 1

[Evgeniia Golovina]

DEXSeq is a good start. :)

There are also other tools for analyzing differential splicing events (exon skipping, alternative exon use, etc).

1. MATS tool for splicing analysis
2. MISO is another popular option
3. cuffQuant and cuffdiff tools (from Cufflinks) also are used to test differential isoform expression

The last two tools (cuffQuant and cuffdiff) are used in differential isoform expression analysis pipeline on http://platform.genestack.org. You need just upload you bam files and run this pipeline.