I am currently attempting to assemble and annotate various regions of unstranded RNA-seq data obtained from paired-end sequencing. I am currently using StringTie for assembly and have come across the option of incorporating the IsoformSwitchAnalyzeR package with the output from StringTie for 3' UTR annotation. I would like to know if I can analyze the assembly results using the IsoformSwitchAnalyzeR package for just one sample. If possible, could you please guide me on the methods I should use? The example code in the quick start guide is not currently applicable to my task.

Best Regards,

Henry