Best tool to find splice variants (composition, fpkm, differential)

Question

[le_xand]

Hi,

I want to find out (for a specific gene) which splice variants are expressed in which sample (I have several samples from different experimental conditions [knock-out, wild type, diet etc.]) I need a tool for RNA-seq data which helps me find the exact splice junctions/exon composition of the isoforms and the expression values (read counts, FPKM etc). So far I've tried CuffDiff and SGSeq (R-package), but my problems were:

CuffDiff (probably) gave me output for every gene and isoforms and I could neither detect the exon composition of the isoform nor which exact gene the isoform belonged to.

SGSeq couldt de novo predict the exons but it often seperated one exon into three and showed me some small introns as exons. Additionally it seems to be very plot centered..

Which tool would be the most useful for my design?

Thanks in advance!

Answer 1

[Kristoffer Vitting-Seerup]

I would recommend IsoformSwitchAnalyzeR ( https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html ) which directly parses cufflinks/cuffdiff output (although other tools such as Kallisto/Salmon/RSEM are also supported) and enables identification of isoform switches with predicted functional consequences where the consequences can be chosen from a long list but includes protein domains etc.

In addition it also nicely summarizes all the Cuffdiff results (the information about all the problems you mention are there - just a bit hidden).

Hope this helps /Kristoffer