Question

I have a file in GFF format and I need to convert it to BED format. What do I do?

Answer 1

Here's a Perl script I wrote if you wanted to do something local.

There's some code in there for translating yeast chromosome names that can be removed, if not needed. I also used a Site feature in the GFF file as the region ID, which might also need tweaking, depending on what features you're interested in.

#!/usr/bin/perl -w

use strict;
use Bio::Tools::GFF;
use feature qw(say switch);

my $gffio = Bio::Tools::GFF->new(-fh => \*STDIN, -gff_version => 2);
my $feature;

while ($feature = $gffio->next_feature()) {
    # print $gffio->gff_string($feature)."\n";

    # cf. http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml
    my $seq_id = $feature->seq_id();   
    my $start = $feature->start() - 1;
    my $end = $feature->end();
    my $strand = $feature->strand();
    my @sites = $feature->get_tag_values('Site');

    # translate strand
    given ( $strand ) {
        when ($_ == 1)  { $strand = "+"; }
        when ($_ == -1) { $strand = "-"; }
    }

    # translate yeast chromosome to UCSC browser-readable chromosome
    # cf. http://www.yeastgenome.org/sgdpub/Saccharomyces_cerevisiae.pdf
    given ( $seq_id ) {
        when ( $_ eq "I" )    { $seq_id = "chr1"; }
        when ( $_ eq "II" )   { $seq_id = "chr2"; }
        when ( $_ eq "III" )  { $seq_id = "chr3"; }
        when ( $_ eq "IV" )   { $seq_id = "chr4"; }
        when ( $_ eq "V" )    { $seq_id = "chr5"; }
        when ( $_ eq "VI" )   { $seq_id = "chr6"; }
        when ( $_ eq "VII" )  { $seq_id = "chr7"; }
        when ( $_ eq "VIII" ) { $seq_id = "chr8"; }
        when ( $_ eq "IX" )   { $seq_id = "chr9"; }
        when ( $_ eq "X" )    { $seq_id = "chr10"; }
        when ( $_ eq "XI" )   { $seq_id = "chr11"; }
        when ( $_ eq "XII" )  { $seq_id = "chr12"; }
        when ( $_ eq "XIII" ) { $seq_id = "chr13"; }
        when ( $_ eq "XIV" )  { $seq_id = "chr14"; }
        when ( $_ eq "XV" )   { $seq_id = "chr15"; }
        when ( $_ eq "XVI" )  { $seq_id = "chr16"; }
        default { }
    }

    # output
    print "$seq_id\t$start\t$end\t$sites[0]\t0.0\t$strand\n";
}
$gffio->close();

To use it:

gff2bed.pl < data.gff > data.bed

Answer 2

Both formats are tab delimited text files used to represent DNA features in genomes. The order of columns between the two are different, there are also columns that correspond to attributes missing from one or the other format. Nonetheless the most important difference between the two is the coordinate systems that they assume.

The BED format developed at UCSC uses a zero based indexing and an open end interval whereas the GFF format developed at Sanger assumes a 1 based coordinate system that includes both start and end coordinates. Therefore

The [0,100] interval in BED format corresponds to [1,100] in GFF format and both are 100 base long. That the first element in BED format will be have the index of 0 where the last 100th element will have the index of 99! Whereas in GFF the first element will have the index of 1 and the last element will have the index of 100.

To convert between the two you may use Galaxy and select the section called Select Formats that will list various transformation options.