How to merge gff3 files?
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4.0 years ago

Hello. I'm new to bioinformatics. I have 11 gff3 files of annotated TE (one for each chromosome of banana). I need to merge them into one gff3 files. Anyone know how to do that?

Thank you :)

gff3 RNA-Seq • 3.6k views
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Your request needs to re-worded to reflect the fact that you have one file each for a chromosome - so what you are really looking for is file "concatenation", not 'merging' :) So the answer below is spot on.

In the future, if you will need to truly 'merge' GFF3 files, then you can look up - BEDTOOLS' utility = merge.

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oh i see! thank you for correcting me :)

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4.0 years ago
skbrimer ▴ 740

if you are using a linux machine can you not just cat *.gff > superbanana.gff I think that should work, the gff files I have worked with in the past didn't have headers so I don't think there is an issue there. Also there is this thread How To Merge Gff Files

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Thank you! I'll try it. Have a nice day :)

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