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

<p>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 <strong>the most important</strong> difference between the two is the coordinate systems that they assume. </p>

<p>The <a href="http://genome.ucsc.edu/FAQ/FAQformat#format1">BED</a> format developed at <code>UCSC</code> uses a zero based indexing and an open end interval whereas the <a href="http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml">GFF</a> format developed at <code>Sanger</code> assumes a 1 based coordinate system that includes both start and end coordinates. Therefore</p>

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

<p>To convert between the two you may use <a href="http://main.g2.bx.psu.edu/">Galaxy</a> and select the section called <code>Select Formats</code> that will list various transformation options.</p>
