How to generate GFF3 or GTF files for a custom reference.

Question

[SDVelivela]

Hi,

I am new to bioinformatics, so this might be a basic question. How can we convert annotated Genbank or Fasta files to GFF3 or GTF format? I need to use FeatureCounts on a BAM file, and my reference is custom-made and can not be downloaded from any databases. How can I make a GFF3 or GTF file for my custom reference?

[GenoMax]

How can we convert annotated Genbank or Fasta files to GFF3 or GTF format?

You can't convert a fasta file to GTF/GFF3 since that is a plain sequence format without any additional information (unless you have information in headers that is useful).

You could also look at making a SAF format file which may be easier to create (e.g. see How to create SAF from text file for FeatureCounts ).

Answer 1

[JC]

my reference is custom-made

What do you have?

a) a new assembly -> then you need to predict/annotate gene models

b) a reference guided genome -> you could try to use the gene models from the original source to map and create a new GTF/GFF, or even do a LiftOver is sequences are not so different

c) if you have a Genbank file with the genes in your custom reference -> you can convert the file to GTF/GFF3

[SDVelivela]

Thank you! A reference made of combining various genes to see what fraction of reads aligned to them. Is there a tool to convert genbank file to GTF?