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DRaw and Observe Multiple enrichment Profiles and Annotation DROMPA

Alternative name: DROMPA3 | DROMPA2

Allows peak calling, visualization, quality check and Polymerase Chain Reaction (PCR) bias filtering of ChIP-seq data. DROMPA calls peaks by comparing the read distribution of the ChIP sample with that of the corresponding input sample. The software identifies peaks as bar graph protein-binding sites when the peaks are sharp (approximately 1 kbp) and when they are broad (approximately 1 Mbp). It can accept multiple mapped reads (reads mapped on multiple loci of the reference genome).

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DROMPA classification

DROMPA specifications

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

DROMPA distribution

versioning

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No versioning.

DROMPA support

Documentation

Maintainers

  • Ryuichiro Nakato <>
  • Katsuhiko Shirahige <>

Additional information

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

Credits

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Publications

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

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.

Link to literature

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