Genome-guided transcriptome reconstruction

Question

[caggtaagtat]

Hi,

I am working with an organsim whose transcriptome is not very well annotated concerning the UTRs. So most annotations in the gtf file reach from start to stop codon. Using RNA-seq data, I would now like to expand the annotations to capture at least some of the UTRs.

For that, I found a method using stringtie according to this github entrie https://github.com/trinityrnaseq/CSHLadvSeqTech/wiki. I'm very new to this kind of analysis and don't know, if there are maybe simple things one has to consider duiring guided transcript reconstruction. For example, would you rather go with trinity or cufflinks?

Any tip is gratefully appreciated :)