naimafahmi/apa-scan

Detection and visualization of annotated and potential Alternative Polyadenylation events

APA-Scan

APA-Scan detects the potential Alternative Polyadenylation (APA) events in the downstream 3'-UTR of a gene among two different biological conditions.

Installation

APA-Scan is a python tool which can be downloaded directly from github. Python (version 3.0 or higher) is required to be installed on users machine to run APA-Scan. It can work on Windows, Linux and Mac platform.

Users need to update the configuration.ini file and run the specific file APA-Scan.py to demonstrate the APA events.

$python3 APA-Scan.py

To generate plots for any selected 3'-UTR region, users need to run makePlots.py and provide input in a specific pattern: chromName:geneName:start-end

$python3 Make-plots.py

User manual

User manual for APA-Scan is available on github https://github.com/compbiolabucf/APA-Scan/blob/master/APA-Scan%20User%20Manual.pdf

Citation

Please use the following information to cite...

Contact the Author

Naima Ahmed Fahmi: [email protected] Wei Zhang: [email protected] Jeongsik Yong: [email protected]