What it does

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

View the modified PeakRanger documentation: http://ranger.sourceforge.net/manualv116.html#introduction

Usage

nr: noise rate estimator. Estimates signal to noise ratio which is an indicator for ChIP enrichment

lc: library complexity calculator. Calculates the ratio of unique reads over total reads. Only accepts bam files.

wig: coverage file generator. Generates variable step format wiggle file

wigpe: coverage file generator. Generates bedGraph format wiggle file and supports spliced alignments and thus only supports bam files

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

ranger: ChIP-Seq peak caller. It is able to identify enriched genomic regions while at the same time discover summits within these regions.

ccat: ChIP-Seq peak caller. Tuned for the discovery of broad peaks

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

Citation

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.

Integration of PeakRanger with Galaxy performed by Ziru Zhou ( ziruzhou@gmail.com ). Please send your comments/questions to help@modencode.org.