Welcome to the UROPA documentation!

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UROPA is a command line based tool intended for genomic region annotation.

Advantages of UROPA

  • Detect the most appropriate annotation of peaks, utilizing parameters such as
    • feature type
    • feature anchor
    • feature direction relative to peak location
    • filtering for attribute values, e.g. “protein_coding”
    • strand specificity
  • Utilization of any available GTF files as annotation reference
  • Multiple queries can be processed in a single run
  • Graduated annotation due to prioritization
  • Multiple output tables (allhits, finalhits, besthits)
  • Visual summary for annotation evaluation
  • Preparation of custom annotation files with the UROPA to GTF utility

How to cite

Please cite the paper describing UROPA when using it in your research: Kondili M, Fust A, Preussner J, Kuenne C, Braun T, Looso M. UROPA: a tool for Universal RObust Peak Annotation. Scientific Reports. 2017;7:2593. doi:10.1038/s41598-017-02464-y.

Contribute

Support

If you have any issue feel free to send an email to Mario Looso

Licence

The project is licensed under the MIT license (see MIT License)

Content of this manual