I've coverage tables generated with StringTie using only the -B option. Can this be used as an input for Ballgown for DGE?
PS: I haven't used the -e option.
-B option is to output for downstream ballgown analysis. Look at your output. If the output from StringTie resulted in .ctab files, then, i guess, you are good to go.
Yes, I have the ctab files as the output. So does the option -e mean only for transcript annotated in the reference genome?