ALLMAPS: How to lift over gene annotations

Within the ALLMAPS run folder, we should be able to see a file with suffix .chain. Let's say our current annotations are in scaffold.gff3, together with the chain file scaffold_to_genome.chain, we can run this command:

$ liftOver -gff scaffold.gff3 scaffold_to_genome.chain genome.gff3 unmapped

The arguments are:

• scaffold.gff3: scaffold annotations (INPUT)
• scaffold_to_genome.chain: translations (INPUT)
• genome.gff3: genome annotations (OUTPUT)
• unmapped: things that fail (OUTPUT)

This command usually runs quickly. Whatever features fail in this operation are placed in the unmapped file, which should always be empty in the case of using ALLMAPS chain file. This command also works on .bed files without the -gff flag.

Download liftOver tool here if you can't locate it on your system: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/