3.0 years ago by
The tool Convert Formats > GFF-to-BED converter will create one BED line per line in the original GFF/GFT dataset. The result is a BED6 dataset (the first 6 columns of full BED format). These are commonly interpreted to be individual "exons" but that is not necessarily the case - the actual BED content depends on the original GFF/GTF input content.
If instead you wish to have a BED12 result (combining regions/exons into a single record - often used to represent a transcript), then there are command-line tools from UCSC available in their Downloads area under Source. For MAC OSX, the location would be here.
Many of these UCSC utilities have been wrapped for Galaxy and are available in the Tool Shed (for use in a local or cloud Galaxy), but I do not believe that the ones needed to produce a BED12 have been yet (gtfToGenePred & genePredToBed). I could be corrected here though!
BED format specification
Hopefully this helps, Jen, Galaxy