phantompeakqualtools protocols

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phantompeakqualtools specifications

Information


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

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Documentation


phantompeakqualtools in pipelines

 (6)
2018
PMCID: 5797644
PMID: 29441061
DOI: 10.3389/fimmu.2018.00030

[…] 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 […]

2018
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 (https://www.encodeproject.org/software/phantompeakqualtools/). macs2 [] algorithm with nucleosome-optimized parameters (−-shift 37 --extsize 73) was applied to call […]

2017
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 (https://code.google.com/p/phantompeakqualtools/). these cross-correlation coefficients are relative measures of the enrichment of the chip data for peak-like distributions […]

2016
PMCID: 4856085
PMID: 26976439
DOI: 10.1534/g3.116.028712

[…] for the chip-seq data sets, we confirmed the quality of data sets by strand cross-correlation (scc) analysis () implemented in the r script “run_spp_nodups.r” packaged in phantompeakqualtools (https://code.google.com/p/phantompeakqualtools/). statistically significant peaks were identified using macs version 2 () with the following essential command line arguments: […]

2015
PMCID: 4598281
PMID: 26390241
DOI: 10.1038/nm.3939

[…] was applied for quality control, and then samtools (http://samtools.sourceforge.net) was used to remove potential pcr duplicates. phantompeak (https://code.google.com/p/phantompeakqualtools/) was applied to estimate the quality and enrichment of the chip–seq dataset. additional encode quality metrics, such as the normalized strand coefficient (nsc) and the relative […]


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phantompeakqualtools in publications

 (22)
PMCID: 5965702
PMID: 29719267
DOI: 10.1016/j.celrep.2018.03.129

[…] flow cells on an illumina nextseq 500 instrument., 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 […]

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

[…] 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 (https://code.google.com/p/phantompeakqualtools) with default parameters (−s = −500:5:1500). for the irreproducible discovery rate (idr) framework, we applied peak detection […]

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 (https://code.google.com/p/phantompeakqualtools/). these cross-correlation coefficients are relative measures of the enrichment of the chip data for peak-like distributions […]

PMCID: 5622369
PMID: 28973448
DOI: 10.1093/nar/gkx648

[…] to extract all reads located within peak regions and compared read counts to those of the unfiltered alignment files. cross-correlation plots were generated for de-duplicated bam files using phantompeakqualtools (), with strand shifts ranging from 0 to 1000 bp at a step size of 5 bp, and otherwise default parameters. we employed ngs.plot () with default parameters to generate aggregation […]

PMCID: 5716146
PMID: 28934481
DOI: 10.1093/nar/gkx618

[…] 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 […]


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phantompeakqualtools review

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Fabien Pichon

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Desktop
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.