Homer findPeaks

For more options, look under: "Command line options for findPeaks"

http://biowhat.ucsd.edu/homer/ngs/peaks.html

TIP: use homer_bed2pos and homer_pos2bed to convert between the homer peak positions and the BED format.

Parameter list

Command line options (not all of them are supported):

Usage: findPeaks <tag directory> [options]

Finds peaks in the provided tag directory.  By default, peak list printed to stdout

General analysis options:
        -o <filename|auto> (file name for to output peaks, default: stdout)
                "-o auto" will send output to "<tag directory>/peaks.txt", ".../regions.txt",
                or ".../transcripts.txt" depending on the "-style" option
        -style <option> (Specialized options for specific analysis strategies)
                factor (transcription factor ChIP-Seq, uses -center, output: peaks.txt,  default)
                histone (histone modification ChIP-Seq, region based, uses -region -size 500 -L 0, regions.txt)
                groseq (de novo transcript identification from GroSeq data, transcripts.txt)
                tss (TSS identification from 5' RNA sequencing, tss.txt)
                dnase (Hypersensitivity [crawford style (nicking)], peaks.txt)

chipseq/histone options:
        -i <input tag directory> (Experiment to use as IgG/Input/Control)
        -size <#> (Peak size, default: auto)
        -minDist <#> (minimum distance between peaks, default: peak size x2)
        -gsize <#> (Set effective mappable genome size, default: 2e9)
        -fragLength <#|auto> (Approximate fragment length, default: auto)
        -inputFragLength <#|auto> (Approximate fragment length of input tags, default: auto)
        -tbp <#> (Maximum tags per bp to count, 0 = no limit, default: auto)
        -inputtbp <#> (Maximum tags per bp to count in input, 0 = no limit, default: auto)
        -strand <both|separate> (find peaks using tags on both strands or separate, default:both)
        -norm # (Tag count to normalize to, default 10000000)
        -region (extends start/stop coordinates to cover full region considered "enriched")
        -center (Centers peaks on maximum tag overlap and calculates focus ratios)
        -nfr (Centers peaks on most likely nucleosome free region [works best with mnase data])
                (-center and -nfr can be performed later with "getPeakTags"

Peak Filtering options: (set -F/-L/-C to 0 to skip)
        -F <#> (fold enrichment over input tag count, default: 4.0)
          -P <#> (poisson p-value threshold relative to input tag count, default: 0.0001)
        -L <#> (fold enrichment over local tag count, default: 4.0)
          -LP <#> (poisson p-value threshold relative to local tag count, default: 0.0001)
        -C <#> (fold enrichment limit of expected unique tag positions, default: 2.0)
        -localSize <#> (region to check for local tag enrichment, default: 10000)
        -inputSize <#> (Size of region to search for control tags, default: 2x peak size)
        -fdr <#> (False discovery rate, default = 0.001)
        -poisson <#> (Set poisson p-value cutoff, default: uses fdr)
        -tagThreshold <#> (Set # of tags to define a peak, default: 25)
        -ntagThreshold <#> (Set # of normalized tags to define a peak, by default uses 1e7 for norm)
        -minTagThreshold <#> (Absolute minimum tags per peak, default: expected tags per peak)

GroSeq Options: (Need to specify "-style groseq"):
        -tssSize <#> (size of region for initiation detection/artifact size, default: 250)
        -minBodySize <#> (size of regoin for transcript body detection, default: 1000)
        -maxBodySize <#> (size of regoin for transcript body detection, default: 10000)
        -tssFold <#> (fold enrichment for new initiation dectection, default: 4.0)
        -bodyFold <#> (fold enrichment for new transcript dectection, default: 4.0)
        -endFold <#> (end transcript when levels are this much less than the start, default: 10.0)
        -fragLength <#> (Approximate fragment length, default: 150)
        -uniqmap <directory> (directory of binary files specifying uniquely mappable locations)
                Download from http://biowhat.ucsd.edu/homer/groseq/
        -confPvalue <#> (confidence p-value: 1.00e-05)
        -minReadDepth <#> (Minimum initial read depth for transcripts, default: auto)
        -pseudoCount <#> (Pseudo tag count, default: 2.0)
        -gtf <filename> (Output de novo transcripts in GTF format)
                "-o auto" will produce <dir>/transcripts.txt and <dir>/transcripts.gtf