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Peakzilla specifications

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Unique identifier OMICS_00454
Name Peakzilla
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data The coordinate files of the mapped reads of the IP and-optionally-control sample.
Input format BED
Output data The TFBSs including the genomic positions, raw, distribution and final score, FDR and a peak number according to each peak’s rank.
Output format BED
Operating system Unix/Linux, Mac OS
Programming languages Python
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Maintainers


  • person_outline Alexander Stark
  • person_outline Jonas Steinmann

Publication for Peakzilla

library_books

Identification of transcription factor binding sites from ChIP-seq data at high resolution.

2013 Bioinformatics
PMCID: 3799470
PMID: 23980024
DOI: 10.1093/bioinformatics/btt470

Peakzilla citations

 (6)
library_books

Modular discovery of monomeric and dimeric transcription factor binding motifs for large data sets

2018
Nucleic Acids Res
PMCID: 5934673
PMID: 29385521
DOI: 10.1093/nar/gky027

[…] hnf4a (sequence read archive accession srr952427, igg: srr952608) () and tfap2a (srr952485,igg: srr952608) (). to find the peaks, the reads were aligned with bwa (), and peak calling was done with peakzilla (). the genome assembly used was grch37 (hs37d5). from each chip-seq peak set, top n = 230 peaks with highest quality score were selected, and for each peak a sequence of length l = 190 bp […]

library_books

Data exploration, quality control and statistical analysis of ChIP exo/nexus experiments

2017
Nucleic Acids Res
PMCID: 5587812
PMID: 28911122
DOI: 10.1093/nar/gkx594

[…] is an important point with implications on the statistical analysis of chip-exo data. specifically, currently available chip-exo specific statistical analysis methods (e.g. mace (), cexor () and peakzilla ()) rely on the existence of peak-pairs formed by forward and reverse strand reads at the binding site. finally, most of current widely used chip-seq quality control (qc) guidelines (–) may […]

library_books

Landscape of histone modifications in a sponge reveals the origin of animal cis regulatory complexity

2017
eLife
PMCID: 5429095
PMID: 28395144
DOI: 10.7554/eLife.22194.055

[…] that contain at least one narrow peak passing a p-value of 0.01. for the diffused histone ptms – h3k36me3 and h3k27me3 – we used the broadpeak representation. rnapii peaks were detected using the peakzilla software (rrid:scr_007471) (), using input dna reads as control (-c 1.5, –s 3). the fraction of reads falling within peak regions (frip) was also calculated (see ). in line with encode […]

library_books

Genome wide identification of Drosophila dorso ventral enhancers by differential histone acetylation analysis

2016
Genome Biol
PMCID: 5037609
PMID: 27678375
DOI: 10.1186/s13059-016-1057-2

[…] all chip-seq enrichment values were calculated as fold change over the corresponding input sample, after normalizing for differences in read count and fragment size. cbp peaks were first called with peakzilla [] using default parameters for the cbp wild-type chip-seq and its corresponding input control. detected peaks were resized to 201 bp centered at the summit, and those with less […]

library_books

Genome Wide Ultrabithorax Binding Analysis Reveals Highly Targeted Genomic Loci at Developmental Regulators and a Potential Connection to Polycomb Mediated Regulation

2016
PLoS One
PMCID: 5004984
PMID: 27575958
DOI: 10.1371/journal.pone.0161997

[…] of the two replicates, demonstrating the reproducibility of the approach. we merged both replicates and identified genomic regions that were significantly enriched for ubx binding (‘peaks’) with peakzilla []. we obtained 5282 peaks (peakzilla score ≥3), of which 1479 peaks were particularly strong with a score ≥5. to control for antibody-specificity and to obtain an estimate […]

library_books

YAP1 Exerts Its Transcriptional Control via TEAD Mediated Activation of Enhancers

2015
PLoS Genet
PMCID: 4546604
PMID: 26295846
DOI: 10.1371/journal.pgen.1005465

[…] two independent biological chip-seq replicates with a pearson correlation coefficient (pcc) of 0.95 (). we identified 2,498 binding sites enriched over matching input using the chip-seq peak-finder peakzilla [] ( and tables). to further benchmark our approach we have analyzed the dataset for the presence of peak regions in the most commonly described yap1 target genes. as anticipated, peaks […]


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Peakzilla institution(s)
Research Institute of Molecular Pathology (IMP), Vienna, Austria; Institute of Molecular Biotechnology (IMBA), Vienna, Austria; Stowers Institute for Medical Research, Kansas City, MO, USA
Peakzilla funding source(s)
Supported by Austrian Ministry for Science and Research through the Genome Research in Austria (GEN-AU) BioinformaticsIntegration Network III; Austrian Research Fund (FWF) (Z_153_B09); NIH New Innovator (1DP2 OD004561-01, a Pew scholar); European Research Council (ERC) Starting Grant from the European Community’s Seventh Framework Programme (FP7/ 2007-2013)/ERC (242922) and Boehringer Ingelheim.

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