Is there a computational tool or possibility to identify mRNA isoforms from the count matrix of a bulk RNA sequencing dataset? I have the counts matrix of an RNA sequencing dataset of fibroblasts and I wish to identify isoforms of a particular gene of interest in it. Can anyone please hint me on a bioinformatics method to achieve this?

In literature, 9 different isoforms of my gene of interest have been reported. My colleague who does the wet lab experiments has identified 3 of those isoforms through western blotting in the fibroblasts that later got sequenced. There might be more isoforms in these fibroblasts.

I will be grateful for any computational hint to identify gene isoforms from my dataset, irrespective if they are differentially expressed or not.

Thank you in advance for your kind help.
You can back to your bam file and use cuffdiff tools it is very able to do your job follow this to liks
http://cole-trapnell-lab.github.io/cufflinks/manual/

https://github.com/Jeanielmj/bioinformatics-workshop/wiki/Differential-Analysis-with-Cuffdiff

My best