UROPA GUI

A Web Platform for genomic region annotation

The annotation of genomic ranges such as peaks resulting from ChIP-seq/ATAC-seq or other techniques represents a fundamental task of bioinformatics analysis with crucial impact on many downstream analyses. In our previous work, we introduced the Universal Robust Peak Annotator (UROPA), a flexible command line based tool which considerably extends the functionality of existing annotation software. In order to reduce the complexity for biologists and clinicians, we have implemented an intuitive web-based graphical user interface (GUI) and fully functional service platform for UROPA. This extension will empower all users to generate annotations for regions of interest interactively.

Features

  • Input: BED file of peaks or other genomic regions
  • Reference: GTF file of desired target features (e.g. genes, transcripts, probes, repeats, …); source = Gencode/Ensembl (102 organisms included) or custom upload
  • Association rules: VERY diverse and easily combinable to a complex ruleset (see Configuration file)
  • Persistence: Unique identifier is created on the server and results will remain available temporarily using the respective link
  • Hosted: Either online on our web server or as a local R Shiny installation

Availability and Implementation

The open source UROPA GUI server was implemented in R Shiny and Python and is available from UROPA_GUI . Please make sure to check loosolab for a comprehensive overview of all our projects and implemented tools.

Try UROPA GUI

The UROPA_GUI contains all necessary data to quickly sample the capabilities of UROPA GUI. * UROPA GUI user guide: Stepwise tutorial.

  • Example data: The following demo GTF and BED files are available on the server. Homo_sapiens.hg19.GRCh37.75_genes_v2.gft -> Human GTF file with reference genes ENCFF001VFA.pol2.sub.bed -> POLR2A ChIP-seq experiment (14989 peaks)

Note

It is mandatory to select filter.attribute before attribute.value. Depending on the GTF file, it might take some time for the attribute.value to be loaded. Please be patient!

How to cite

  • Kondili M, Fust A, Preussner J, Kuenne C, Braun T, and Looso M. UROPA: a tool for Universal RObust Peak Annotation. Scientific Reports 7 (2017), doi: https://www.nature.com/articles/s41598-017-02464-y
  • Hendrik Schultheis, Jens Preussner, Annika Fust, Mette Bentsen, Carsten Kuenne, Mario Looso: UROPA: A Web Platform for genomic region annotation

License

This project is licensed under the MIT license.