UROPA - Universal RObust Peak Annotator

UROPA (‘Universal RObust Peak Annotator’) 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.

Features

Detect the most appropriate annotation with flexible parameter 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
Utilization of all available GTF files as annotation database
One run with variable 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
Preparation of custom annotation files

Documentation

A detailed description of how to apply UROPA to your data can be found here.

Installation and Command-line usage

Make sure all prerequisites are met:

R/Rscript (v3.3.0 or higher, follow instructions on url)
Python (v2.7.8-anaconda-2.1.0)
- Choose Anaconda-2.1.0-Linux-x86 or -x86_64,
- Install with bash Anaconda2-4.2.0-Linux-x86_64.sh,
- Follow instructions and type 'yes' to prepend Anaconda to PATH in your .bashrc file,
- or type after installation: $export PATH=/home/<user>/anaconda/bin:$PATH
htslib (1.3.2 or higher, follow instructions on url)
- cd htslib-1.3.2/
- ./configure
- make
- make install or sudo make prefix=/home/<user>/htslib install

Install required packages for R:

install.packages(c("ggplot2", "devtools", "gplots", "gridExtra", "jsonlite", "VennDiagram"))
source("https://bioconductor.org/biocLite.R")
biocLite(c("RBGL","graph"))

# To install the last required package-Vennerable, devtools has to be loaded to use the install from github function
# if you copy this and want to use it in once, 
# make sure the library loading is not interrupted by the question if present packages should be updated

library(devtools)
install_github("jenzopr/Vennerable")

Install UROPA locally by running:

git clone https://github.molgen.mpg.de/loosolab/UROPA.git
export PATH=$PATH:dir/to/uropa/uropa.py

Usage: uropa.py [options]          

Available options:
	
	- h, --help             print this help message and further details on the configuration file
        - i, --input            filename of configuration file
        - o, --output           directory for results and prefix of the output file name
        - r, --reformat         create an additional compact and line-reduced table as result file
        - s, --summary          filename of additional visualisation of results in graphical format
        - t n, --threads n      multiprocessed run: n = number of threads to run annotation process
        --no-comment            do not show comment lines in output files
        - l, --log              log file name for messages and warnings
        - d, --debug            print verbose messages (for debugging purposes)
        - v, --version          print the version and exit

How to cite

Kondili M, Fust A, Preussner J, Kuenne C and Looso M. UROPA: a tool for Universal RObust Peak Annotation. (in preparation)

Contribute

Source Code here
Issue Tracker here

Support

If you have any questions please feel free to contact Mario Looso (mario.looso@mpi-bn.mpg.de).

License

The project is licensed under the MIT License.

mariakondili/UROPA