For doing an RNA-seq analysis, I used STAR for mapping reads to the genome followed by Stringtie for genome-guided assembly. I downloaded the GTF file of my organism (a plant) and merged it with the annotation file produced by Stringtie for Cuffdiff analysis. (I don't want to use ballgown package). I used cuffdiff from cufflinks-2.2.1 package for differential expression analysis. But among the cuffdiff outputs, just gene_exp.diff and isoform_exp.diff are filled with results and splicing.diff, promoters.diff and cds_exp.diff are empty. As I searched, I found the below command to obtain the combined.gtf file that contains tss_id and p_id, required for getting splicing.diff and promoter.diff results from cuffdiff analysis.
cuffcompare -s /path/to/genome_seqs.fa -CG -r annotation.gtf annotation.gtf
I was wondering if I can use the merged GTF file produced by Stringtie along with original GTF file in the above command?