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Question: Join/Combine gff3 or gtf files
0
gravatar for deshpande.neha2
2.4 years ago by
deshpande.neha2 • 0
deshpande.neha2 • 0 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 COMMENT • link •
modified 2.4 years ago by mike-zx • 260 • written 2.4 years ago by deshpande.neha2 • 0
1
gravatar for mike-zx
2.4 years ago by
mike-zx • 260
mike-zx • 260 wrote:
cat file1.gff3 file2.gff3 >> combined.gff3

That cat syntax should give you what you want Hope this helps
ADD COMMENT • link modified 2.4 years ago • written 2.4 years ago by mike-zx • 260
1

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

ADD REPLY • link written 2.4 years ago by swbarnes2 ♦ 9.6k

This worked. Thank you!

ADD REPLY • link written 2.4 years ago by deshpande.neha2 • 0
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