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
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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
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One run with variable sets of parameters by multiple queries
-
Graduated annotation due to priorization
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Different easily-readable output tables (allhits, finalfits, besthits).
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Visual summary for annotation evaluation
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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:
- Python
- download Anaconda for Linux version Python 2.7 to direction where python should be installed
- run
bash Anaconda2-4.3.0-Linux-x86_64.sh
- Answer the question "Do you wish the installer to prepend the Anaconda2 install location to PATH in your /home/.../.bashrc ?" with yes
OR do
PATH=dir/to/python_anaconda:$PATH
after installation process - run
conda install -c bioconda pysam
- R/Rscript (v3.3.0 or higher; follow instructions on url)
- install required packages step by step:
install.packages(c("ggplot2", "devtools", "gplots", "gridExtra", "jsonlite", "VennDiagram")) source("https://bioconductor.org/biocLite.R") biocLite(c("RBGL","graph")) # to install the last required package, devtools has to be loaded to use the install from github function library(devtools) install_github("jenzopr/Vennerable")
- Git: run
bash sudo apt-get install git
Install UROPA locally
git clone https://github.molgen.mpg.de/loosolab/UROPA.git
export PATH=$PATH:dir/to/uropa
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 [mandatory]
-p, --prefix prefix for output files, can include subdirectories [basename of --input]
-r, --reformat create an additional compact and line-reduced table as result file
-s, --summary additional visualisation of results in graphical format will be created
-t n, --threads n multiprocessed run: n = number of threads to run annotation process
-add-comments show comment lines in output files explaining the columns
-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, Braun T, and Looso M. UROPA: a tool for Universal RObust Peak Annotation. Scientific Reports 7 (2017), doi: 10.1038/s41598-017-02464-y
Contribute
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.