combine twi files : .gtf file (from cufflinks) and .gff file (from augustus) for Augustus gene prediction

Question

[Mehmet]

Hi all

I have a .gtf file (transcripts.gtf) from cufflinks and a .gff file (bam2gff from augustus). I combined these two files by using cat command on unix. Now, I want to use the combined file for gene prediction. For this, What do I need to do?

Thanks

[Mike]

I know it's been almost 7 years, but can you please elaborate what did you end up doing? I have a similar situation- instead of cufflinks I used stringTie and got the BAM files from STAR aligner. Thanks!