What is the best tool for isoform function prediction?
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5.7 years ago
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Hi, there are many databases where are functional annotations only for genes. I want to make analysis of my RNA-seq data and identify exact isoform function (biological process and subcellular localization). Is there any instrument for that?

Thanks in advance!

RNA-Seq isoform prediction • 2.1k views
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You might want to take a look at the Trinnotate workflow. It could give you some ideas: https://trinotate.github.io/

Which tool generated your isoforms?

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They used pretty old tools like HMMER, signalP, tmHMM and RNAMMER. I hope there is better tool for functional isoform analysis. And trinity doesn't analyze isoforms.

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It would be tricky to assign functions in isoform (also same for noncoding regions) specific manner. Since most of isoforms or alternate exon usage is more tissue/ disease or condition dependent. I would rather suggest you to use the gene product (Geneids) of those isoforms for enrichment analysis / Gene Ontology. Then select the interesing terms related to you study, if the term shows as significant. Later do isoform specific functional studies (experiment) for the genes of interest.

If you are interested in using up-to-date database for gene level enrichemnt analysis, you are welcome to use GeneSCF which is real-time based enrichment analysis tool.

For finding or predicting isoforms from your RNA-seq,

1)

A: How to determine alternative splicing read counts

2) i would also suggest you new pipeline HISAT2 -> StringTie -> Ballgown

http://www.nature.com/nprot/journal/v11/n9/full/nprot.2016.095.html

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