phantompeakqualtools statistics

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phantompeakqualtools specifications


Unique identifier OMICS_00431
Name phantompeakqualtools
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format BAM, BED
Output format BED
Operating system Unix/Linux
Programming languages R
License MIT License
Computer skills Advanced
Version 1.1
Stability Stable
Maintained Yes




No version available


phantompeakqualtools citations


High Resolution Epigenomic Atlas of Human Embryonic Craniofacial Development

Cell Rep
PMCID: 5965702
PMID: 29719267
DOI: 10.1016/j.celrep.2018.03.129
call_split See protocol

[…] ChIP-seq reads were aligned to the human genome (hg19) using Bowtie2 (version [v.] 2.2.5) (). Fragment sizes of each library were estimated using PhantomPeakQualTools (v.1.14) (). Histone modification-enriched regions were identified and annotated using Hypergeometric Optimization of Motif Enrichment (HOMER, v.4.8.3) (). Reproducibly enriched r […]


Consequences of early life stress on genomic landscape of H3K4me3 in prefrontal cortex of adult mice

BMC Genomics
PMCID: 5836825
PMID: 29504911
DOI: 10.1186/s12864-018-4479-2

[…] trimmomatic [] adapter removal tool and mapped to GRCm38/mm10 mouse reference genome using bowtie2 aligner []. The quality metrics of ChIP-seq libraries (Additional file : Table S1) were assessed by phantompeakqualtools software ( MACS2 [] algorithm with nucleosome-optimized parameters (−-shift 37 --extsize 73) was applied to call both […]


Profiling of Human Molecular Pathways Affected by Retrotransposons at the Level of Regulation by Transcription Factor Proteins

Front Immunol
PMCID: 5797644
PMID: 29441061
DOI: 10.3389/fimmu.2018.00030

[…] ler algorithm using BWA software. Concatenation of fastq files with single-end or pairwise reads, alignment to the reference genome, and filtering were done using BWA, Samtools, Picard, Bedtools, and Phantompeakqualtools software. The aligned TFBS were mapped on the RE sequences annotated by RepeatMasker and downloaded from the USCS Browser (RepeatMasker table). TFBS occurrence data were extracted […]


High intensity UV laser ChIP seq for the study of protein DNA interactions in living cells

Nat Commun
PMCID: 5670203
PMID: 29101361
DOI: 10.1038/s41467-017-01251-7

[…] ts) and overlapping reads were removed. Strand cross-correlation (SCC) analysis and computation of NSC (normalized strand coefficient) and RSC (relative strand coefficient) values was performed using phantompeakqualtools ( with default parameters (−s = −500:5:1500). For the Irreproducible Discovery Rate (IDR) framework, we applied peak detection by SP […]


Identification of genome wide targets of Olig2 in the adult mouse spinal cord using ChIP Seq

PLoS One
PMCID: 5648140
PMID: 29049317
DOI: 10.1371/journal.pone.0186091

[…] divided by the total number of reads that aligned to exactly one location. The normalized strand cross-correlation coefficient and relative strand cross-correlation coefficient were calculated using phantompeakqualtools ( These cross-correlation coefficients are relative measures of the enrichment of the ChIP data for peak-like distributions of rea […]


Automatic identification of informative regions with epigenomic changes associated to hematopoiesis

Nucleic Acids Res
PMCID: 5716146
PMID: 28934481
DOI: 10.1093/nar/gkx618
call_split See protocol

[…] le cell lymphomas (MCL) from BLUEPRINT (see ). The BAM files were converted to BED format and duplicate reads were removed for all the experiments. We computed different quality control measures with phantompeakqualtools v1.10.1 () including total number of reads, normalized strand cross-correlation coefficient (NSC) and quality tag based on thresholded relative strand cross-correlation coefficien […]


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phantompeakqualtools review

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Fabien Pichon

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Indispensable for ChIP-seq and ATAC-seq quality control. Produces a graph showing the crosscorrelation of reads distributions on forward and reverse strand as well as ratios to estimate the noise. Be carefull however, because these ratios are meaningfull only for narrow peaks, not for broad peaks like H3K27me3 or H3K36me3.