I've got some RNAseq data that I'm looking at to quantify and identify which splice variants of a gene are expressed under different conditions. I've used cummeRbund to show that there are some splice variants expressed differentially, but I can't tell which ones those are because they're just labeled with a TCONS ID. How can I use the TCONS ID to get the coding sequence/exon-exon junctions of an isoform?
Thanks!
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spencernystrom •
1 answer
I know the question is quite old but I'd like to add an answer for future reference.
If you are interested in isoform switches a potential tool could be 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.
Hope this helps /Kristoffer
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