Rat ( rn6 ), Zebrafish ( danRer7 ), Fruit fly ( dm3 ), and C. elegans ( ce10 ). Loading Custom Genomes
Ensure the homer/bin directory is added to your executable PATH so you can run commands from any directory. homer download genome
loadGenome.pl -name MyCustomGenome -org null -fasta genome.fasta -gtf genes.gtf Use code with caution. Rat ( rn6 ), Zebrafish ( danRer7 ), Fruit fly ( dm3 ), and C
Check which genomes are currently available for download. perl /path-to-homer/configureHomer.pl -list Use code with caution. loadGenome
To download and install a genome for , you primarily use the configureHomer.pl script. This script manages the software's suite of pre-configured organism, promoter, and genome packages. Core Commands for Downloading Genomes
If your specific genome is not in the default list, you can load your own using the loadGenome.pl script. This requires a file for the sequence and a GTF file for gene annotations. Example Command: