PeakRanger protocols

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description
PeakRanger computational protocol

PeakRanger specifications

Information


Unique identifier OMICS_00451
Name PeakRanger
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Parallelization MapReduce
Computer skills Advanced
Stability Stable
High performance computing Yes
Maintained Yes

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Documentation


Publication for PeakRanger

PeakRanger IN pipelines

 (3)
2017
PMCID: 5496309
PMID: 28676099
DOI: 10.1186/s13072-017-0140-6

[…] data were controlled for general quality features using fastqc. unambiguously mapped and unique reads were kept for subsequent generation of binding profiles and calling of peaks using macs and peakranger [52] using reads derived from sequencing of input dna as control. peaks were called at p < 10−5 and fdr <5%. all downstream analyses were done in r/bioconductor […]

2014
PMCID: 4371837
PMID: 25250711
DOI: 10.7554/eLife.04235.017

[…] set for both. the data sets were then swapped and analyzed for regions with decreased levels of h3k27me3. to get the reads for histograms shown in figure 1—figure supplement 3a, the ‘wig’ module of peakranger parsed all aligned reads and counted reads within the specified regions. to find the rest-binding motif (re1), rest peak coordinates were used as input for fimo (grant et al., 2011). […]

2012
PMCID: 3411736
PMID: 22879999
DOI: 10.1371/journal.pone.0042483

[…] samtools were used to sort, remove, and duplicate the sequence reads [17]. filtered reads were aligned to the human reference genome (hg19) form ucsc. the aligned reads were passed to macs [18] and peakranger [19] for peak calling, with the total input dna background used in each comparison. macs and peakranger software were used to find regions (peaks) with statistically significant enrichment […]

PeakRanger institution(s)
Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, USA; Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY, USA; Ontario Institute for Cancer Research, MaRS Centre, Toronto, ON, Canada; Institute for Genomics & Systems Biology, The University of Chicago, Chicago, IL, USA
PeakRanger funding source(s)
This project was funded by the iPlant Collaborative and a grant from the National Science Foundation Plant Cyberinfrastructure Program (#DBI-0735191).

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