Extracting features from .gff3 file based on position

Question

[adamerum]

Hi everyone,

Can anyone point me in the direction of how I can extract all features within a given genomic range from a .gff3 file? For example, if I have a list of genomic regions I am interested in, with scaffold ID and start to end position - how can I extract the gene IDs from the gff?

I am extremely new to bioinformatics so please excuse me if this is super straightforward or has been answered elsewhere...

I have found posts where you can use Bioconductor packages to extract features based on ID (i.e. searching for a specific gene) but can't see how to extract all genes in a given range.

The number of tools out there are overwhelming and I am pretty sure this is the kind of straightforward thing someone could easily answer!

Thanks in advance.

[Juke34]

You can filter your gff to keep only the region of interest as indicated here.

Then 2 possibilities using AGAT:

1. You could use something like agat_convert_sp_gff2tsv.pl

   And then extract what you need from the tsv:

   awk '{if( $3=="gene") print $10}' your_file.tsv
   

   where $10 is the 10th column (considering the ID is in the 10th column, check the first line to see in which column the |D is)

2. Use agat_sp_extract_attributes.pl:

   agat_sp_extract_attributes.pl --gff input.gff -t gene --attribute ID
   

[adamerum]

Thank you both for your replies - great to be made aware of bedtools and AGAT which both look very helpful!

[Ram]

You should be able to use bedtools - it works on GFF files. The "list of genomic regions" should be a BED file (0-based).