RNA-Seq isoforms identification

Question

[latita.atun]

Hi

I'm new to this and I want someone to guide me on which is the best tool to detect isoforms in RNA-seq data.

[Ram]

Quantify known isoforms or detect novel transcripts?

[Andres]

What are you trying to find?, are you working with an organism that has an available genome?. What kind of data you have?. I think you probably have illumina data.

It sounds that you need to annotate genes. either in a genome or denovo. If you have a genome you pass the rna-seq data either raw or aligned to the genome to a gene modeler/annotator software, and then in the output you can check if any isoform was found. I had used BREAKER2 in the past for this. Check this to know more. If denovo you would have to assemble transcriptome first, and use it as a "reference".

Other way may be to align reads (with an RNA aware aligner like STAR or many others) to the genes you want to check for isoforms and manually check for isoform signals in a visualization software like IGV or tablet. This would be hard.