• Introduction
• System Requirement
• Obtaining PeakRanger
• Compiling PeakRanger from source codes
  • Compiling in Ubuntu
  • Compiling in Mac OSX
  • Compiling in Windows
  • HTML support
• Synopsis
• Command line options
  • nr
    • input
    • Qualities
    • Other
  • lc
    • input
    • Other
  • wig
    • input
    • Output
    • Qualities
    • Other
  • wigpe
    • input
    • Output
    • Qualities
    • Other
  • ranger
    • input
    • Output
    • Qualities
    • Running modes
    • Other
  • ccat
    • input
    • Output
    • Qualities
    • Other
• Using the gene annotation module
• Output files
  • lc
  • nr
  • wig
  • wigpe
  • ranger
  • ccat

Introduction

PeakRanger is a multi-purporse software suite for analyzing next-generation sequencing (NGS) data. The suite contains the following tools:

1. nr noise rate estimator. Estimates signal to noise ratio which is an indicator for ChIP enrichment
2. lc library complexity calculator. Calculates the ratio of unique reads over total reads. Only accepts bam files.
3. wig coverage file generator. Generates variable step format wiggle file
4. wigpe coverage file generator. Generates bedGraph format wiggle file and supports spliced alignments and thus only supports bam files
5. ranger ChIP-Seq peak caller. It is able to identify enriched genomic regions while at the same time discover summits within these regions.
6. ccat ChIP-Seq peak caller. Tuned for the discovery of broad peaks

Both ranger and ccat supports generating HTML-based annotation reports.

wigpe can also generate coverage files for bam files containing spliced reads, such as those from RNA-Seq experiments.

If you use PeakRanger in your research, please cite:

Feng X, Grossman R, Stein L: PeakRanger:A cloud-enabled peak caller for ChIP-seq data.BMC Bioinformatics 2011, 12(1):139.

if you use the ccat tool, please also cite:

Xu, H., L. Handoko, et al. (2010).A signal-noise model for significance analysis of ChIP-seq with negative control.Bioinformatics 26(9): 1199-1204.

System Requirement

1. The ranger and ccat tool depends on the R programming environment to generate HTML reports. But they can run without it, even with --report and --gene_annot_file set.
2. When the number of peaks called by ranger or ccat is huge, it takes a while for user's browser to parse the generated HTML file.
3. The lc tool needs about 1.7G ram per 10 million aligned reads.

Obtaining PeakRanger

PeakRanger can be downloded from sourceforge.

Compiling PeakRanger from source codes

Synopsis

peakranger lc sample.bam

peakranger nr --format bam sample.bam control.bam

peakranger wig --format bam sample.bam sample.bam_coverage

peakranger wig --format bed sample.bed sample.bed_coverage

peakranger wigpe sample.bam sample.bam_coverage

peakranger wigpe sample.bam sample.bam_coverage_splitted -s

peakranger wigpe sample.bam sample.bam_coverage_splitted_by_strand -sx

peakranger wigpe sample.bam sample.bam_coverage_gzipped -z

peakranger wigpe sample.bam sample.bam_coverage_splitted_by_strand_gzip -sxz

peakranger wigpe sample.bam sample.bam_coverage_read_extend_to_200 -l 200

peakranger ranger --format bam sample.bam control.bam ranger_result

peakranger ranger --format bam sample.bam control.bam ranger_result_threaded_faster -t 3

peakranger ccat --format bam sample.bam contro.bam ccat_result

peakranger ccat --format bam sample.bam contro.bam ccat_result_with_HTML_report
--report --gene_annot_file hg19refGene.txt
peakranger ccat --format bam sample.bam contro.bam ccat_result_with_HTML_report_5kb_region
--report --gene_annot_file hg19refGene.txt
--plot_region 10000

Command line options

Using the gene annotation module

for ranger and ccat, users can generate HTML reports for called peaks by using:

--report --gene_annot_file sample_data/gene_annotation_files/dm3refGene.txt

in the sample_data folder, we provide annotation files for hg19, dm3 and mm9. Users can download annotations of other species from UCSC' genome browsers.

Output files