Is there a computational tool or possibility to identify mRNA isoforms from the count matrix of a bulk RNA sequencing dataset?
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