I am trying to assemble/join gff3 or gtf files from 2 different organisms to use as a reference for Stringtie. How do I do that? I tried using the cat command but I end up getting an output file which is exactly the first of the 2 gff3 files.
For example cat file1.gff3 >> file2.gff3 > combined.gff3 gives me an output combined.gff3 which is exactly file1.gff3
What can I do?