Where to get a reference gene model in bed fomat? Is the only option converting it from gtf to bed?

Question

[pubsurfted]

basically the title.

And if the only option is indeed converting a gtf to bed, can you list down some recommeded tools?

Best wishes.

[Matthias Zepper]

Download from the UCSC Table Browser or use the respective converters in the binary utilities: GTF/GFF3 -> GenePred -> BED.

Answer 1

[alejandrogzi]

If you are struggling to append gene-related features to a GTF file converted from a BED file this tool could be an option: bed2gtf. Just need an isoforms file to map each line and append gene features.