UGENE integrates the Cistrome workflow for analysis of ChIP-Seq data. The workflow requires reference data to be present in the UGENE data folder. Reference data for human are provided in the NGS package and in the can be installed via the Online Installer. To configure them manually download the data from the "Download UGENE and components" page and web page http://ugene.net/download-all.html and unpack to the "cistrome" folder inside the UGENE data folder.
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