Hello Biostars,

I have a question about stringtie and how it assigns reads to a specific transcript isoform.

I wanted to perform a Differential Expression analysis using a genome assembly without a gene annotation, as a reference. To do this I have aligned the reads using STAR and then pooled all the alignments into a single bam file. To assemble the transcripts and annotate the reference I used stringtie.

After this I used the gtf output of stringtie as a reference to calculate the abundance for each individual sample using the -e option.

What I am wondering is this: When having two transcript isoforms that largely share the exon positions, how does stringtie decide to which to assign a read pair?