Hi, I just run into HOMER and want to do motif discovery on MACS-returned peaks. I use the following command line on linux machine: findMotifsGenome.pl path-to-bedfile/my-bed-file HOMER/data/genomes/mm9 <output directory="">
According to the protocol, I need to download mm9 first. I use this command line to download mm9 genome sequence: perl configureHomer.pl -install mm9.
I checked the directory: HOMER/data/genomes/mm9 Under this directory I have a bunch of files:
annotations/ chr15.fa chr1.fa chr5.fa chr9.fa chrY_random.fa mm9.rna
chr10.fa chr16.fa chr1_random.fa chr5_random.fa chr9_random.fa conservation/ mm9.splice3p
chr11.fa chr16_random.fa chr2.fa chr6.fa chrM.fa mm9.aug mm9.splice5p
chr12.fa chr17.fa chr3.fa chr7.fa chrUn_random.fa mm9.basic.annotation mm9.stop
chr13.fa chr17_random.fa chr3_random.fa chr7_random.fa chrX.fa mm9.full.annotation mm9.tss
chr13_random.fa chr18.fa chr4.fa chr8.fa chrX_random.fa mm9.miRNA mm9.tts
chr14.fa chr19.fa chr4_random.fa chr8_random.fa chrY.fa mm9.repeats preparsed/
I check each fasta file and they indeed have sequence :)
But when I run the command to do motif discovery, there is an error message saying:
ls: cannot access HOMER/data/genomes/mm9/preparsed//mm9.*.cgbins: No such file or directory
Could not find background files for 200 bp fragments
I also try the subdirectory of mm9: preparsed/. It doesn't work as well.
Any suggestion is appreciated. Thanks a lot.
Hi, Have you got rid of this error and if so then how? Because i am coming across same type of error!!
Thanks