phantompeakqualtools protocols

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.3 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.4 the aligned tfbs were mapped on the re sequences annotated by repeatmasker5 and downloaded from the uscs browser6 (repeatmasker table). tfbs occurrence data […]

2018
PMCID: 5836825
PMID: 29504911
DOI: 10.1186/s12864-018-4479-2

[…] [30] adapter removal tool and mapped to grcm38/mm10 mouse reference genome using bowtie2 aligner [31]. the quality metrics of chip-seq libraries (additional file 1: table s1) were assessed by phantompeakqualtools software (https://www.encodeproject.org/software/phantompeakqualtools/). macs2 [32] algorithm with nucleosome-optimized parameters (−-shift 37 --extsize 73) was applied to call […]

2018
PMCID: 5836825
PMID: 29504911
DOI: 10.1186/s12864-018-4479-2

[…] genome using bowtie2 aligner [31]. the quality metrics of chip-seq libraries (additional file 1: table s1) were assessed by phantompeakqualtools software (https://www.encodeproject.org/software/phantompeakqualtools/). macs2 [32] algorithm with nucleosome-optimized parameters (−-shift 37 --extsize 73) was applied to call both broad and narrow peaks from the pooled data. public sequencing […]

2017
PMCID: 5253667
PMID: 28112213
DOI: 10.1038/srep41063

[…] −10 while for multi-mapping reads alignment score was set equal or greater than −10. the quality of chip-seq data was evaluated following encode quality metrics (https://code.google.com/archive/p/phantompeakqualtools/) and the numerical values obtained are provided in supplementary table s1. the cross-correlation analysis resulted in good nsc and rsc values, obtained using the code from dr. […]

2017
PMCID: 5253667
PMID: 28112213
DOI: 10.1038/srep41063

[…] in supplementary table s1. the cross-correlation analysis resulted in good nsc and rsc values, obtained using the code from dr. kundaje at stanford university (https://code.google.com/archive/p/phantompeakqualtools/) cited by encode consortium (http://genome.ucsc.edu/encode/encodetools.html). moreover, we obtained average pbc scores. irreproducible discovery rate procedure (idr v 2.0.2) […]

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.