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.