by Jan Grau, Stefan Posch, Ivo Grosse, and Jens Keilwagen
ChIPper is a universal tool for de-novo motif discovery. ChIPper has successfully been applied to ChIP-seq, ChIP-exo and protein-binding microarray (PBM) data.
We provide ChIPper as a public web-server, a web-application that can be installed in a local Galaxy server, and as a command line program.
ChIPper is available as a public web-server at galaxy.informatik.uni-halle.de.
ChIPper is implemented in Java using Jstacs. You can download the command line application as a Jar. In addition, we provide the Jar of the Galaxy web-application for installing it in your local Galaxy server.
ChIPper will be part of the next public release of the Jstacs library.
Running the command line application
For running the command line application, Java v1.6 or later is required.
The arguments of the command line application have the following meaning: