DROMPA3 README

1. Overview

DROMPA (DRaw and Observe Multiple enrichment Profiles and Annotation) is a program for user-friendly and flexible ChIP-seq pipelining. DROMPA can be used for quality check, PCRbias filtering, normalization, peak calling, visualization and other multiple analyses of ChIP-seq data. DROMPA is specially designed so that it is easy to handle, and for users without a strong bioinformatics background.

2. Install

DROMPA is written in C and requires the following programs and libraries:

• Cairo libraries
• GTK library
• GNU Scientific Library
• zlib
• SAMtools (for BAM/CRAM formatted input)
• R (for PROFILE command)

2.1. Install required libraries

On Ubuntu:

 sudo apt install git gcc libgtk2.0-dev libgsl-dev samtools

On CentOS:

 sudo yum -y install zlib-devel gsl-devel gtk2-devel

On Mac:

 brew tap brewsci/bio
 brew install gsl gtk cairo pkgconfig samtools

2.2. Install cpdf

DROMPA uses Coherent PDF for merging pdf files.

 git clone https://github.com/coherentgraphics/cpdf-binaries

2.3. Install DROMPA

git clone https://github.com/rnakato/DROMPA3
cd DROMPA3
make

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

2.4. Add the PATH environment variable

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

export PATH = $PATH:$HOME/DROMPA3:$HOME/cpdf-binaries/Linux-Intel-64bit/

2.5 Docker image

DROMPA and SSP are also probatively available on Docker Hub.

To obtain a docker image for DROMPA and SSP, type:

docker pull rnakato/ssp_drompa

3. Usage

See Manual.pdf for detail. Please direct bug reports and questions about usage to [email protected].

4. Troubleshooting

• If you get an error "invalid chr name: XXX" when using parse2wig, the chromosome name XXX contained in the input file is absent in genometable file you specified by -gt. Please check the genometable file.
• If it is necessary to output ChIP/Input enrichment distribution (e.g. for yeast), please use -outputwig option in drompa_peakcall, which can generate the wig files of ChIP/Input enrichment and p-values.

5. Citation

1. Nakato, R. and Shirahige K., Statistical Analysis and Quality Assessment of ChIP-seq Data with DROMPA, pp. 631–643, Springer New York, New York, NY, 2018.

2. Nakato R., Shirahige K., Recent advances in ChIP-seq analysis: from quality management to whole-genome annotation, Briefings in Bioinformatics, 2016.

3. Nakato, R., Itoh T. and Shirahige K., DROMPA: easy-to-handle peak calling and visualization software for the computational analysis and validation of ChIP-seq data, Genes to Cells, vol.18, issue 7, 2013.