Homer: Different Outputs

Question

[GeneInfo]

Hi, In order to find the instances of motif showing up in the peak file, I have tried two scripts from HOMER: findmotifsGenome.pl and annotatePeaks.pl. However, the number of instances of that motif is totally different. For example, in the motif discovery results from knownResult.html file: TF-A has 2000 binding sites. In the annotatePeaks.pl, it has 6000 sites. [based on 21st column: when empty, it means the peak is not bound by TF-A] In the findmotifsGenome.pl, it has 4000sites. Any idea? Thanks.

Answer 1

[thakkar.bjl]

Hello,

I find one problem while using Homer to findMotifs.pl

I have a number of sequences while I am giving that as a input findMotifs.pl observed this type of error. Can you explain me what I have to give, because I am not able to understand which background file this script want.

Selected Options:
    Input file = rice_G2_l1_to_4_1kbp_DEG_match_4143
    Promoter Set = fasta
    Output Directory = motif_result
    background file: rice_G2_l1_to_4_1kbp.fasta

    !Warning - no background FASTA file specified (Highly recommended)
    !Your input sequences will be randomized to serve as a background instead.

sh: scrambleFasta.pl: command not found
    Parsing FASTA format files...
sh: fasta2tab.pl: command not found
sh: cleanUpSequences.pl: command not found
sh: cleanUpPeakFile.pl: command not found
sh: fasta2tab.pl: command not found
sh: cleanUpSequences.pl: command not found
sh: cleanUpPeakFile.pl: command not found
sh: makeBinaryFile.pl: command not found

    Progress: Step4 - removing redundant promoters

    Progress: Step5 - adjusting background sequences for CpG content...
sh: homerTools: command not found
sh: freq2group.pl: command not found
sh: assignGeneWeights.pl: command not found
rm: cannot remove `motif_result/0.569837599135102cgfreq.tmp': No such file or directory

    Normalizing lower order oligos using homer2
sh: homer2: command not found

    Progress: Step6 - Gene Ontology Enrichment Analysis
    Skipping...

    Progress: Step7 - Known motif enrichment
sh: findKnownMotifs.pl: command not found

    Progress: Step8 - De novo motif finding (HOMER)
sh: homer2: command not found
sh: homer2: command not found
sh: homer2: command not found
cat: motif_result/homerMotifs.motifs*: No such file or directory
sh: compareMotifs.pl: command not found
    Job finished

Thanks.

[Mikael Huss]

Your problem is not the background file (that is just a warning that does not halt the program) but that the program can't find the commands it needs. Most likely, you haven't added the location of the HOMER executables to the PATH variable on your system. Please refer to the installation instructions: http://homer.salk.edu/homer/introduction/install.html