DROMPA protocols

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DROMPA specifications

Information


Unique identifier OMICS_00438
Name DROMPA
Alternative names DRaw and Observe Multiple enrichment Profiles and Annotation, DROMPA3, DROMPA2
Software type Package/Module
Interface Command line interface
Restrictions to use None
Output data A protein-binding profile map.
Output format PNG, PDF
Operating system Unix/Linux
Programming languages C
Computer skills Advanced
Version 3.2.6
Stability Stable
Requirements
Cairo libraries, GTK library, GNU Scientific Library, zlib, SAMtools (for BAM formatted input), R
Source code URL http://www.iam.u-tokyo.ac.jp/chromosomeinformatics/rnakato/drompa/archives/
Maintained Yes

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Documentation


Maintainers


  • person_outline Ryuichiro Nakato <>
  • person_outline Katsuhiko Shirahige <>

Additional information


Testing version of DROMPA3: https://github.com/rnakato/DROMPA3

Publication for DRaw and Observe Multiple enrichment Profiles and Annotation

DROMPA in pipeline

2015
PMCID: 4626154
PMID: 26503909
DOI: 10.3892/mmr.2015.4249

[…] peaks identified using the refseq database were compared with genomic regions of lncrnas from noncode version 4.0 database (http://www.noncode.org/). images of peak visualization were obtained using drompa 2.3.1 version software ()., genomic locations of cpg islands were downloaded from ucsc (https://genome.ucsc.edu/) (). genomic regions of each peak were compared with those of cpg islands […]


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DROMPA in publications

 (15)
PMCID: 5815096
PMID: 29253234
DOI: 10.1093/nar/gkx1260

[…] from chip experiments were mapped with bwa's ‘mem’ algorithm () using default settings to the galgal5 version of the chicken genome downloaded from ensembl release 86. chip peaks were called using drompa2 () using a window size of 100 000 bp and a smoothing window of 200 000 bp. drompa2’s internal poisson test was disregarded by setting its p-value cutoff to 1. the fancd2-chip […]

PMCID: 5696371
PMID: 29158484
DOI: 10.1038/s41467-017-01807-7

[…] uniquely mapped reads; redundantly mapped reads (reads starting exactly at the same 5′-sequence ends) were filtered out for further analysis. for peak calling and data visualization, we used drompa (version 2.6.4 with 1-kbp bin). to compare multiple chip-seq data, chip and input reads were both normalized with the total number of mapped reads. the identified peaks satisfied the following […]

PMCID: 5450002
PMID: 28620275
DOI: 10.3389/fnins.2017.00307

[…] calling was performed using macs software (zhang et al., ; feng et al., ) in version 2.1.1, using the nomodel option at a q-value threshold of <0.1. for visualization of peaks on the genomic map, drompa2 tool (nakato et al., ) was used. peaks that overlapped among different samples were calculated using bedtools (quinlan and hall, ) and drompa2 (nakato et al., ). as for defining the consensus […]

PMCID: 5413336
PMID: 28408410
DOI: 10.1084/jem.20161517

[…] aligned to the mouse reference sequence (mm9) using bowtie2 version 2.1.0 () with default options. after filtering duplicated reads, peak calling and chip-seq data visualization were performed by drompa version 2.5.1 (). to calibrate chip-seq data for rad21, we used the method described by . the whole-cell extract from the mouse cortex was mixed with whole-cell extract from human rpe cells, […]

PMCID: 5384234
PMID: 28387373
DOI: 10.1038/srep46228

[…] v2.1.0 with default parameters. mapped reads in a 100-bp bin were summed along each chromosome, followed by filtration of duplicate reads and normalization with the total mapped read number by drompa2 v2.5.1. data reproducibility was measured by calculating chip read intensities ±1 kbp around pth2a peaks identified by drompa2 with the “-pthre1 5e-2 -qthre 5e-2” option. calculated read […]


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DROMPA institution(s)
Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan; CREST, JST, K’s Gobancho, Tokyo, Japan; School and Graduate School of Bioscience and Biotechnology and Bio-Frontier Research Center, Tokyo Institute of Technology, Yokohama, Japan
DROMPA funding source(s)
Supported by a Grant-in-Aid for Young Scientists, Grant-in-Aid for Scientific Research on Innovative Areas, CREST, a Research Program of Innovative Cell Biology by Innovative Technology and Grant-in-Aid for Scientific Research.

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