Join/Combine gff3 or gtf files

Question

[deshpande.neha2]

Hi,

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?

Answer 1

[n,n]

cat file1.gff3 file2.gff3 >> combined.gff3

That cat syntax should give you what you want Hope this helps

[swbarnes2]

The header from file2 is going to be in the middle of your combined gff. You might want to fix that.

[deshpande.neha2]

This worked. Thank you!