I used stringtie ballgown pipeline for my data analysis. I am trying to categorize my differentially expressed transcript in novel and known using gffcomapre. During categorization, I found some MSTRGs are marked as semi-novel, some marked as novel, and some are not present in tmap file of gffcompare. So, now I am confused with those MSTRGs which are not present in gffcomapre output.
Should we consider them Novel? If not, how we can validate their categories as novel, semi-novel or known?
I used stringtie ballgown pipeline for my data analysis. I am trying to categorize my differentially expressed transcript in novel and known using gffcomapre. During categorization, I found some MSTRGs are marked as semi-novel, some marked as novel, and some are not present in tmap file of gffcompare. So, now I am confused with those MSTRGs which are not present in gffcomapre output. Should we consider them Novel? If not, how we can validate their categories as novel, semi-novel or known?