Question: Join/Combine gff3 or gtf files
0
gravatar for deshpande.neha2
2.4 years ago by
deshpande.neha20 wrote:

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?

sequencing rna-seq genome • 2.0k views
ADD COMMENTlink modified 2.4 years ago by mike-zx260 • written 2.4 years ago by deshpande.neha20
1
gravatar for mike-zx
2.4 years ago by
mike-zx260
mike-zx260 wrote:
cat file1.gff3 file2.gff3 >> combined.gff3

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

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by mike-zx260
1

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

ADD REPLYlink written 2.4 years ago by swbarnes29.6k

This worked. Thank you!

ADD REPLYlink written 2.4 years ago by deshpande.neha20
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