Hi, thank you so much for putting together this method! I just want to clarify something I’m confused about: when generating the combined GTF for Salmon quantification, does the GTF only contain the last exons and UTRs (or intron) regions, or does it contain the full isoforms? For intronic APA, if the quantification only uses the last exons with extended intronic regions, how does PAPA deal with exons that might be shared by other isoforms?
Hi, thank you so much for putting together this method! I just want to clarify something I’m confused about: when generating the combined GTF for Salmon quantification, does the GTF only contain the last exons and UTRs (or intron) regions, or does it contain the full isoforms? For intronic APA, if the quantification only uses the last exons with extended intronic regions, how does PAPA deal with exons that might be shared by other isoforms?