Welcome to the UROPA documentation!¶
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)