Hi I get FPKM for gene (not transcript) from stringtie by these parameter: -e -G -A. I also use htseq (default parameter )to generate counts matrix for the same gene sets and calculate fpkm using R. The gtf I used in this two method is the same. However the result fpkm is not the same. It seems that the overall fpkm generated by htseq is lower than stingtie. I try to use stringtie to get counts matrix for each gene but stringtie seems not generate count for gene level. I have searched the difference between them but I didn't find any answers. Thank you very much for helping me!