CistromeFinder README


The CistromeFinder data portal can help investigators query, evaluate and visualize binding sites of more than 400 trans-acting factors. CistromeFinder includes records of more than 5,400 public ChIP-seq assays from NCBI (SRA), EBI (ENA), ENCODE or Epigenome Roadmap project. These records are organized in a meta-information database. The dataset quality control and binding site evaluation system are combined into a pipeline to acquire overall performance of each ChIP-seq assay and enrichment for each binding site. CistromeFinder has a user interface to query, examine, evaluate and visualize data. It is further well integrated with popular applications such as UCSC genome browser, Primer3Plus and CistromeMap.


  • cd <root directory of ChIP-Finder project>
  • $ python setup.py install
  • $ pserve cps_production.ini

Then the ChIP-Finder can be used in your specified binding port in cps_production.ini


Our web portal can be accessed at http://cistrome.org/finder.

For more details, please check our paper which will be published hopefully late this year.