DROMPAplus

0. Changelog

See Changelog

1. Overview

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 written in C++ and has many valuable features. 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.

See http://drompaplus.readthedocs.io/ for the detailed Manual.

2. Install

2.1. Docker image

We recommend to use the latest Docker image of DROMPAplus from DockerHub.

2.1.1. Docker

To use docker command, type:

docker pull rnakato/ssp_drompa
docker run -it --rm rnakato/ssp_drompa drompa+

Note: When using the docker image, it is necessary to mount the directory by -v option to access the input files as follows:

docker run -it --rm -v $(pwd):/mnt rnakato/ssp_drompa parse2wig+ \
         -i /mnt/ChIP.bam -o ChIP --odir /mnt/parse2wigdir+ --gt /mnt/genometable.txt

This command mounts the current directory to /mnt directory in the container. Please see also the document of Docker.

2.1.2. Singularity

Singularity can also be used to execute the docker image:

singularity build ssp_drompa.sif docker://rnakato/ssp_drompa
singularity exec ssp_drompa.sif drompa+

Singularity mounts the current directory automatically. If you access the files in the other directory, please mount by --bind option, for instance:

singularity exec --bind /work ssp_drompa.sif drompa+

This command mounts /work directory.

2.2. Building from source

2.2.1 Requirements

DROMPAplus requires the following programs and libraries:

• Boost C++ library (>1.53.0)
• Cairo libraries
• GTK library
• GNU Scientific Library (>1.15)
• zlib (>1.2.7)
• CMake (>2.8)
• HTSlib (1.10.2) (for SAM/BAM/CRAM formatted input)

and also contains two submodules:

• SSP
• Coherent PDF

2.2.2. Install required libraries

On Ubuntu:

sudo apt install git build-essential libgtkmm-3.0-dev libboost-all-dev \
libz-dev libbz2-dev libgsl-dev libcurl4-gnutls-dev cmake

On CentOS:

sudo yum -y install git gcc-c++ clang boost-devel zlib-devel gsl-devel gtkmm30-devel bzip2-devel cmake

On Mac:

 brew install gsl gtk gtkmm cairo pkgconfig curl xz zlib boost cmake

2.2.3. Install DROMPAplus

git clone --recursive https://github.com/rnakato/DROMPAplus
cd DROMPAplus
make

If you get an installation error, make sure that all required libraries are successfully installed.

2.2.4. Add the PATH environment variable

Permanently set the path to the DROMPAplus download directory by updating your ~/.bashrc file. For example, if you downloaded DROMPAplus into $HOME directory, add the following lines to ~/.bashrc:

export PATH=$PATH:$HOME/DROMPAplus/bin:$HOME/DROMPAplus/otherbins

3. Reference

For DROMPAplus:

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

For DROMPA:

• Nakato R, Shirahige K., Statistical Analysis and Quality Assessment of ChIP-seq Data with DROMPA, Methods in Molecular Biology, 2018.