Is stringtie able to distinguish endogenous from exogenous transcript? #501
Description
We are generating targeted RNA sequencing data using Nanopore in THP-1 cells and are interested in using stringtie for downstream analysis.
These cells express the endogenous transcript as well as wildtype and mutant transcript (exogenous) of the same gene. Both constructs contain a 24-base FLAG tag at the C-terminus, and the mutant construct additionally carries a single nucleotide change. As a result, the exogenous transcripts differ slightly from the endogenous version.
Would stringtie be able to distinguish between endogenous and exogenous transcripts based on these sequence differences? If so, are there specific reference or alignment considerations we should be aware of.