Welcome to the UROPA documentation!
UROPA is a command line based tool, intended for genomic region annotation. Based on a configuration file, different target features can be prioritized with multiple integrated queries. These can be sensitive for feature type, distance, strand specificity, feature attributes (eg. protein_coding) or the anchor position relative to the feature. UROPA can incorporate reference annotation files (GTF) from different sources, like Gencode, Ensembl, or RefSeq, as well as custom reference files produced by the user.
Advantages of UROPA
- Simple usage: No programming
- Utilization of all available GTF files as annotation database
- Detect the most appropriate annotation with flexible keys that allow robustness and simple customization, such as
- feature type
- feature anchor
- feature direction relative to peak location
- filter for attribute values, e.g. "protein_coding"
- strand specificity
- Preparation of custom annotation files
- One run with multiple sets of parameters by multiple queries
- Graduated annotation due to priorization
- Different easily-readable output tables (AllHits, FinalHits, BestperQuery_Hits).
- Visual summary for annotation evaluation
- Annotation with default values
How to cite
Please cite the paper describing UROPA when using it in your research: tba
Contribute
Source Code here
Further details see here
Support
If you have any issue feel free to send an email to Maria Kondili (maria.kondili@mpi-bn.mpg.de)
Licence
The project is licensed under the MIT license