Where to get a reference gene model in bed fomat? Is the only option converting it from gtf to bed?
basically the title.
And if the only option is indeed converting a gtf to bed, can you list down some recommeded tools?
Best wishes.
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alejandrogzi •
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pubsurfted •
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pubsurfted •
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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.
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Download from the UCSC Table Browser or use the respective converters in the binary utilities:
GTF/GFF3 -> GenePred -> BED.