How to merge two gff3 files?
1
0
Entering edit mode
9 months ago
Light92 ▴ 60

Hello everyone, I'm looking for a script or a tool able to merge two gff3 files, made as follows:

1) A file containing annotation data for my species

2) Another file with additional annotation (information obtained later, trying to annotate the genome against another organism in order to give a function to more genes)

The coordinate system of the two gff3s is the same since both the gff3s are produced starting from the genome of my species of interest.

Anything I found seems to be outdated, thanks in advance for your help!

gff3 merge • 423 views
ADD COMMENT
1
Entering edit mode
9 months ago

I use AGAT for that and many other GFF processing things as well.

AGAT - Another Gff Analysis Toolkit

ADD COMMENT
0
Entering edit mode

Hi, thanks for your answer, what script do you use exactly?

agat_sp_merge_annotations.pl ?

ADD REPLY
1
Entering edit mode

depends on what exactly you want to achieve but yes, agat_sp_merge_annotations.pl sounds about right.

alternatively you can first cat both gff files together and then run agat_convert_sp_gxf2gxf.pl to fix the 'issues' .

On their github page there are lots of explanations and guidelines on what to use when. There are likely also different routes that lead to the same result.

ADD REPLY

Login before adding your answer.

Traffic: 1655 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6