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.