I am trying to design an experiment to do differential experiment analysis on two breeds of one species and compare them. I have been suggested to do alternative splicing analysis and look for different variants using RNA-seq as well. The genome of the animal I am working with has been assembled, and I have access to its gff file. Do I need to do alternative splicing analysis in addition to differential expression as well? Also, please recommend software to do alternative splicing analysis for RNA-seq.