DROMPAplus: a pipeline tool for ChIP-seq analysis

DROMPA (DRaw and Observe Multiple enrichment Profiles and Annotation) is a ChIP-seq pipeline tool that meets various needs, including quality check, analysis, and visualization of multiple ChIP samples.

DROMPAplus is an update of DROMPA3. It is written in C++ and runs from a single launch command on conventional Linux systems.

  • The main features of DROMPAplus are summarized below. DROMPAplus:

    • Accepts multiple map file formats (SAM, BAM, CRAM, Bowtie, TagAlign(.gz)) and read distribution formats (WIG(.gz), bigWig, bedGraph).

    • Supports spike-in normalization and total read normalization.

    • Outputs various quality metrics for ChIP-seq analysis.

    • Visualizes read distributions in conventional PDF format; therefore, no additional programs are required which is preferable for many users, especially when sharing results (e.g., on cloud storage) with collaborators who do not have a strong bioinformatics background.

    • Automatically estimates the fragment length from single-end reads using SSP.

    • Can visualize two samples in a single line, which delineates the co-occurrence (e.g., H3K4me3 and H3K27ac) and exclusivity (e.g., H3K27me3 and H3K36me3) of read enrichment. Transparency (alpha) of read color can be specified.

    • Supports chromatin loops from ChIA-PET (Mango format) and Hi-C (HICCUPS format) with colors corresponding to the p-values.

    • Bases the HEATMAP command on Python3, which enables flexible customization.


Fig. 1 Schematic representation of DROMPA+ features and functionality.



  • Nakato R., Sakata T., Methods for ChIP-seq analysis: A practical workflow and advanced applications, Methods, 2020.



rnakato AT iqb.u-tokyo.ac.jp