Hi. I am using HOMER bioinformatics software and I am running into an issue when trying to analyze repeats. I need to load a genome for pombe yeast (ASM294v2.47).
I've attempted to load the genome using this code:
perl pathToHomer/HOMER/bin/loadGenome.pl –name spombe1 –fasta pathToGenome/PombeFullGenome.fa –gtf pathToGTF/Schizosaccharomyces_pombe.ASM294v2.47.gtf –org null
but I get this output:
Current Settings: Genome name = FASTA file = GTF file = Organism = Version = custom Genome will be stored in directory: pathToHomer/HOMER//data/genomes// !! Options -name, -fasta, -gtf, and -org are REQUIRED !! Program will prepare a custom genome for use with HOMER Usage: loadGenome.pl <Required Parameters ...> [options] NOTE: If your genome is available at UCSC, consider using the update scripts located in the pathToHomer/HOMER//update directory Required Parameters: -name <genome name> (i.e. hg19, tair10, etc.) -fasta <genome fasta file> (Single genome sequence, preferrabley soft masked, unzipped) -gtf <gene annotation file> (Transcript annotation in gtf format, -gff/-gff3 to use them) (Always best to use a gtf file whenever possible, gffs can be organized differently.. .) -org <organism name, ok to use 'null'> Other options: -force (Overwrite any existing genome with the same name) -promoters <promoter set name> (Create promoter set with genome and gtf files) -id <idtype> (options: gene, refseq, unigene, ensembl, or custom, default: custom) -version <version id> (Assign version, versions starting with 'v' are managed by the configureHomer.pl script and my be overwritten, default: custom) -gid (Use gene_id instead of transcript_id to identify the transcripts from GTF files) -tid (Use transcript_id instead of gene_id to identify the transcripts from GTF files, default) -ensemblRepeats <GFF3 file> (gff3 annotations from ensembl usually have repeat definitions to o)
So I don't think the command is executing properly. I've also tried:
perl pathToHomer/HOMER/configureHomer.pl -install pombe
And it runs but I don't see "pombe" anywhere.
When I try to run analyzeRepeats, it doesn't run.