I am making my first UCSC assembly hub to display a non-UCSC annotated genome within the browser. All is well except that I cannot work out how to add the gene annotation, which is currently in GFF3 format. I am aware that track hubs only except the "big" file versions, so presumably a bigBed version of the annotation is required. Does anyone know of a handy method of converting GFF3 to BED/bigBED? I think BED12 is required I to retain the differentiation between CDS, UTR and introns...
P.S. I have Googled this! Convert .Gff3 File To 12-Column .Bed File is a help, but I would be interested to know if there have been developments since then.
GTF or GFF2 can be used for gene annotation!