I used Hisat2, Stringtie and Ballgown to perform differential analysis on my data. I followed the tutorial in the HISAT, StringTie, and Ballgown paper and everything went fine until I used Ballgown to extract genes and transcripts with q-value less than 0.05. I got 293 significantly differentially expressed genes but only 112 significantly differentially expressed transcripts, which doesn't make sense to me. I believe there should be more significantly differentially expressed transcripts than genes since one gene correspond to at least one transcript.
My question is: is it possible to have more differentially expressed genes than transcripts? Or maybe I made some mistakes in my analysis. Any thoughts are extremely valuable to me.
My data has two conditions and each condition has three biological replications.
I am totally new to RNA-Seq and differential analysis so I am sorry if my question is stupid.
Thank you in advance.