I have created the following output files by using the stringtie tool 1) Output GTF file containing the assembled transcripts by stringtie

2) A merged GTF file from all sample GTF
3)ballgown input files

I am not sure which of the above file is used further for Gene Ontology by using tool DAVID or agriGO. This output file I have to create? The output file taken from the manual is as:-

  ...Gene ID     Gene Name   Reference   Strand  Start   End     Coverage    FPKM        TPM
  NM_000451   SHOX        chrX        +       624344  646823  0.000000    0.000000    0.000000
  NM_006883   SHOX        chrX        +       624344  659411  0.000000    0.000000    0.000000

Am I supposed to pick the gene Id and expression value to find gene ontology results? Or there is something else I need to do.