Repeat Enrichment Estimator

This tool aims to measure the enrichment of annotated repeat types in ChIP-seq data. A more detailed description of the method and an application to the repetitive elements associated with histone modifications in human and mouse cells can be found in the following paper.

Daniel S Day, Lovelace J Luquette, Peter J Park and Peter V Kharchenko. Estimating enrichment of repetitive elements from high-throughput sequence data. Genome Biology (In press). doi:10.1186/gb-2010-11-6-r69
The tool is currently supplied with repeat assemblies for human, mouse and drosophila. More may be available in the future or on request. The assemblies can be downloaded here:

Download: Human hs36 (590MB)     Mouse mm9 (539MB)     Drosophila dm3 (40MB)     Source code (at your own risk)

Please do not submit more than one analysis at a time.


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View a demo of the tool

We have constructed a demo and tutorial to walk new users through a precomputed example analysis. During the demo, you may not upload or delete data or analyses--you will need to register a full account to analyze your data.