NarrowPeaks protocols

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NarrowPeaks specifications

Information


Unique identifier OMICS_00449
Name NarrowPeaks
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, R
License Artistic License version 2.0
Computer skills Advanced
Version 1.24.0
Stability Stable
Requirements
R(>=2.10.0), BiocGenerics, IRanges, GenomicRanges, splines, S4Vectors, GenomeInfoDb, fda, CSAR, ICSNP, rtracklayer, BiocStyle
Maintained Yes

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NarrowPeaks in pipeline

2017
PMCID: 5446763
PMID: 28549443
DOI: 10.1186/s12920-017-0274-1

[…] both the human and mouse tdp-43 iclip data have been previously published [, ].table 1 , processed eclip data (previously described by []) was downloaded from the encode project. the narrowpeaks bed format was used with the first nucleotide of the cluster defined as the peak. peak coordinates from iclip and eclip were converted to the hg38 and mm10 builds using the liftover tool […]


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NarrowPeaks in publications

 (9)
PMCID: 5785525
PMID: 29371630
DOI: 10.1038/s41598-018-20043-7

[…] sequencing. we used model-based analysis for chip-seq (macs) with input dna as a control, to identify the following two types of regions of enrichment: (1) narrow peaks of contiguous enrichment (narrowpeaks) that pass a poisson p-value threshold of 0.00001 (macs v1.4.2, default parameters), and (2) broader regions of enrichment (broadpeaks) that pass a q-value threshold of 0.05 (broad peak […]

PMCID: 5752390
PMID: 29053670
DOI: 10.3791/56136

[…] projects., note: the protocol can be paused anywhere., obtain a bed, peaks format, or bigwig file containing the data to be input into genome. the file should have extension name "bed", "broadpeaks""narrowpeaks", or "bigwig" respectively. ‚Äčnote: zipped versions of these type of files will also work., use an internet browser to go to genemo.org. any operating system capable of running […]

PMCID: 5446763
PMID: 28549443
DOI: 10.1186/s12920-017-0274-1

[…] both the human and mouse tdp-43 iclip data have been previously published [, ].table 1 , processed eclip data (previously described by []) was downloaded from the encode project. the narrowpeaks bed format was used with the first nucleotide of the cluster defined as the peak. peak coordinates from iclip and eclip were converted to the hg38 and mm10 builds using the liftover tool […]

PMCID: 5389510
PMID: 27980063
DOI: 10.1093/nar/gkw1276

[…] motif analysis was performed using opossum 3.0 (). for motif analysis, mcf10a- or mcf7-specific brd4-bound broadpeaks from macs2 were intersected with rnapii-bound broadpeaks and then with rnapii narrowpeaks. mcf7-specific brd4-enriched regions were used as background sequences for finding mcf10a-specific motifs and vice-versa. jaspar core profiles were used as motif database. genes proximal […]

PMCID: 5137422
PMID: 27492288
DOI: 10.1093/nar/gkw691

[…] settings as for the real chip-seq data. finally, we assessed the mapping bias and excluded the biased sites if the imbalance ratio of any allele was greater than 60%., uniformly processed chip-seq narrowpeaks were downloaded from encode (). in order to increase the confidence of tf-bound regions, we narrowed the peaks to the 100 base pairs (bp) core regions centered around the peak max […]


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