This is a wrapper for findMotifsGenome.pl from HOMER but not all options are included.

Program will find de novo and known motifs in regions in the genome.

Usage:

findMotifsGenome.pl <pos file> <genome> <output directory> [additional options]

Example:

findMotifsGenome.pl peaks.txt mm8r peakAnalysis -size 200 -len 8

Possible Genomes:

        -- or --
Custom: provide the path to genome FASTA files (directory or single file)
        Heads up: will create the directory "preparsed/" in same location.

Basic options:

-mask (mask repeats/lower case sequence, can also add 'r' to genome, i.e. mm9r)
-bg <background position file> (genomic positions to be used as background, default=automatic)
        removes background positions overlapping with target positions unless -keepOverlappingBg is used
        -chopify (chop up large background regions to the avg size of target regions)
-len <#>[,<#>,<#>...] (motif length, default=8,10,12) [NOTE: values greater 12 may cause the program
        to run out of memory - in these cases decrease the number of sequences analyzed (-N),
        or try analyzing shorter sequence regions (i.e. -size 100)]
-size <#> (fragment size to use for motif finding, default=200)
        -size <#,#> (i.e. -size -100,50 will get sequences from -100 to +50 relative from center)
        -size given (uses the exact regions you give it)
-S <#> (Number of motifs to optimize, default: 25)
-mis <#> (global optimization: searches for strings with # mismatches, default: 2)
-norevopp (don't search reverse strand for motifs)
-nomotif (don't search for de novo motif enrichment)
-rna (output RNA motif logos and compare to RNA motif database, automatically sets -norevopp)

Scanning sequence for motifs:

-find <motif file> (This will cause the program to only scan for motifs)

Known Motif Options/Visualization:

-mset <vertebrates|insects|worms|plants|yeast|all> (check against motif collects, default: auto)
-basic (just visualize de novo motifs, don't check similarity with known motifs)
-bits (scale sequence logos by information content, default: doesn't scale)
-nocheck (don't search for de novo vs. known motif similarity)
-mcheck <motif file> (known motifs to check against de novo motifs,
-float (allow adjustment of the degeneracy threshold for known motifs to improve p-value[dangerous])
-noknown (don't search for known motif enrichment, default: -known)
-mknown <motif file> (known motifs to check for enrichment,
-nofacts (omit humor)
-seqlogo (use weblogo/seqlogo/ghostscript to generate logos, default uses SVG now)

Sequence normalization options:

-gc (use GC% for sequence content normalization, now the default)
-cpg (use CpG% instead of GC% for sequence content normalization)
-noweight (no CG correction)
Also -nlen <#>, -olen <#>, see homer2 section below.

Advanced options:

-h (use hypergeometric for p-values, binomial is default)
-N <#> (Number of sequences to use for motif finding, default=max(50k, 2x input)
-local <#> (use local background, # of equal size regions around peaks to use i.e. 2)
-redundant <#> (Remove redundant sequences matching greater than # percent, i.e. -redundant 0.5)
-maxN <#> (maximum percentage of N's in sequence to consider for motif finding, default: 0.7)
-maskMotif <motif file1> [motif file 2]... (motifs to mask before motif finding)
-opt <motif file1> [motif file 2]... (motifs to optimize or change length of)
-rand (randomize target and background sequences labels)
-ref <peak file> (use file for target and background - first argument is list of peak ids for targets)
-oligo (perform analysis of individual oligo enrichment)
-dumpFasta (Dump fasta files for target and background sequences for use with other programs)
-preparse (force new background files to be created)
-preparsedDir <directory> (location to search for preparsed file and/or place new files)
-keepFiles (keep temporary files)
-fdr <#> (Calculate empirical FDR for de novo discovery #=number of randomizations)

homer2 specific options:

-homer2 (use homer2 instead of original homer, default)
-nlen <#> (length of lower-order oligos to normalize in background, default: -nlen 3)
        -nmax <#> (Max normalization iterations, default: 160)
        -neutral (weight sequences to neutral frequencies, i.e. 25%, 6.25%, etc.)
-olen <#> (lower-order oligo normalization for oligo table, use if -nlen isn't working well)
-p <#> (Number of processors to use, default: 1)
-e <#> (Maximum expected motif instance per bp in random sequence, default: 0.01)
-cache <#> (size in MB for statistics cache, default: 500)
-quickMask (skip full masking after finding motifs, similar to original homer)
-minlp <#> (stop looking for motifs when seed logp score gets above #, default: -10)

Original homer specific options:

-homer1 (to force the use of the original homer)
-depth [low|med|high|allnight] (time spent on local optimization default: med)