BroadPeak statistics

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BroadPeak specifications

Information


Unique identifier OMICS_00433
Name BroadPeak
Software type Package/Module
Interface Command line interface
Restrictions to use None
Output data A file of the genomic locations of broad peaks.
Output format BED
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline I. King Jordan <>

Publication for BroadPeak

BroadPeak in pipeline

2018
PMCID: 5802526
PMID: 29317610
DOI: 10.1038/s41398-017-0053-y

[…] stem cell-derived neurons were generated by the epigenomics roadmap. preprocessed broad peak calls for h3k4me3 were downloaded from http://egg2.wustl.edu/roadmap/data/byfiletype/peaks/consolidated/broadpeak/. peaks with a negative log10 p-value of 5 or greater were retained for further analysis, as described in the original macs protocol., h3k4me3 chip-sequencing data from neun-positive […]


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BroadPeak in publications

 (33)
PMCID: 5828245
PMID: 29482603
DOI: 10.1186/s13073-018-0523-8

[…] data availability: , data generated by the roadmap epigenomics project were downloaded from http://egg2.wustl.edu/roadmap/data/byfiletype/peaks/consolidated/broadpeak/dnase/, http://egg2.wustl.edu/roadmap/data/byfiletype/peaks/consolidated/broadpeak/ , http://egg2.wustl.edu/roadmap/data/byfiletype/peaks/consolidated/narrowpeak/ , blueprint monocyte […]

PMCID: 5805369
PMID: 29377896
DOI: 10.1371/journal.pgen.1007186

[…] to improve disease risk prediction performance []., we used tissue-specific snp annotations from the encode [] and the roadmap [] projects in the present study. specifically, we downloaded the broadpeak files from the roadmap epigenomics web portal (http://egg2.wustl.edu/roadmap/web_portal/). the broadpeak files contain peak regions for four histone marks (h3k27me3, h3k36me3, h3k4me1, […]

PMCID: 5785525
PMID: 29371630
DOI: 10.1038/s41598-018-20043-7

[…] parameters), and (2) broader regions of enrichment (broadpeaks) that pass a q-value threshold of 0.05 (broad peak mode of macs v2.1.0). for the broad-range histone marker, h3k27me3, we used the broadpeak representation of macs v2.1.0 peak caller., we designed four different guide rnas (grnas) targeting a 20-bp site (protospacer) in the human cdh1 locus that precedes an ngg trinucleotides, […]

PMCID: 5780744
PMID: 29363429
DOI: 10.1186/s12864-017-4339-5

[…] transcriptional target genes were predicted from promoter (additional file : figure s7)., ctcf chip-seq data for monocytes cd14+ cells (gsm1003508_hg19_wgencodebroadhistonemonocd14ro1746ctcfpk.broadpeak.gz), cd4+ t cells (srr001460.bam), cd20+ b cells (gsm1003474_hg19_wgencodebroadhistonecd20ctcfpk.broadpeak.gz), h1-hesc (wgencodeawgtfbsutah1hescctcfunipk.narrowpeak.gz), ipsc (gse96477), […]

PMCID: 5943035
PMID: 29648536
DOI: 10.7554/eLife.33084.053

[…] (version 0.1.19)(). properly-paired reads only were selected for further analysis., chip and input reads from each individual were used to call peaks in each individual using macs2 () with the broadpeak option at various qvalue cut-offs. a lenient threshold of qvalue = 0.1 was used in subsequent analysis to maximize the number of regions identified in each species., to determine […]


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BroadPeak institution(s)
School of Biology, Georgia Institute of Technology, Atlanta, GA, USA; Buck Institute for Age Research, Novato, CA, USA; PanAmerican Bioinformatics Institute, Santa Marta, Magdalena, Colombia
BroadPeak funding source(s)
Supported by Alfred P. Sloan Research Fellowship in Computational and Evolutionary Molecular Biology [BR-4839] and Buck Institute Trust Fund.

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