How To Generate Background Files For Homer Motif Discovery

Question

[GeneInfo]

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.

[Ram]

Hi, Have you got rid of this error and if so then how? Because i am coming across same type of error!!

Thanks

Answer 1

[Mikael Huss]

I have run this command successfully on mm9. These are the contents of my "preparsed" folder:

[mikaelh]$ ls $HOME/software/homer/data/genomes/mm9/preparsed/

mm9.200.cgbins  mm9.200.cgfreq  mm9.200.gcbins  mm9.200.pos  mm9.200.seq

Is it the same for you? Perhaps you are missing some files.

Alternatively - although I guess you have made sure that this is not the case - perhaps you have accidentally given the wrong path? The command that you give

findMotifsGenome.pl path-to-bedfile/my-bed-file HOMER/data/genomes/mm9

will of course only work if the HOMER directory is in your current working directory.

[GeneInfo]

Hi Mikael, Thanks for your comment.

I only have one mm9.200.pos in my preparsed folder. Actually I have tried to download mm9 with this command for several times, everytime I get different dataset in the preparsed folder: perl configureHomer.pl -insall mm9

BTW, from the manual, it seems HOMER need to locate the mm9 genome sequence in /data/genomes/mm9 not in //data/genomes/mm9/preparsed/

I am not sure what happened when I download mm9.

Also, I have trouble setting up Ghostscript. If you remembered the installation process.... After I use the following command: ./configure make

configuration is successful and make command will give me some error messages in the end.

Anyway, Thanks a lot.

[Mikael Huss]

Yes, I installed the mm9 stuff in the same way, by running configureHomer.pl with -install mm9. I am not sure why you are getting different results each time. Maybe time to contact the developer directly?

Yes, the genome sequence is in the directory you indicate but the error message you received was about the background frequency files. For what it's worth, here are the contents of my $HOMER_PATH/data/genomes/mm9 folder:

[mikaelh]$ ls

annotations chr19.fa chr8.fa mm9.full.annotation chr10.fa chr1.fa chr8_random.fa mm9.miRNA chr11.fa chr1_random.fa chr9.fa mm9.repeats chr12.fa chr2.fa chr9_random.fa mm9.rna chr13.fa chr3.fa chrM.fa mm9.splice3p chr13_random.fa chr3_random.fa chrUn_random.fa mm9.splice5p chr14.fa chr4.fa chrX.fa mm9.stop chr15.fa chr4_random.fa chrX_random.fa mm9.tss chr16.fa chr5.fa chrY.fa mm9.tts chr16_random.fa chr5_random.fa chrY_random.fa preparsed chr17.fa chr6.fa conservation chr17_random.fa chr7.fa mm9.aug chr18.fa chr7_random.fa mm9.basic.annotation

I already had Ghostscript installed so I didn't run into problems with that. If you got error messages with 'make', it sounds like that is definitely where you should start trying to fix things.

Answer 2

[qyyuan]

Hi, I met the same problem and I solve it by this: findMotifsGenome.pl my.bed /home/Software/Homer/data/genomes/hg19 <output directory=""> -preparsedDir