AS-Quant generates the quantification level of different types of alternative splicing events between two biological conditions and assesses the significant of the events.
AS-Quant tool can be downloaded/cloned directly from github. Users need to have python3 installed on their machine. It can work both on Windows and Linux platform.
Users will need to run the as-quant.py file in order to demonstrate the AS events. $python3 as_quant.py
To generate plot for a specific exon, users need to run make_plots.py and provide input in a specific pattern: chrom:geneName:start-end $python3 make_plots.py
User manual for AS-Quant is available on github https://github.com/compbiolabucf/AS-Quant/blob/main/AS-Quant_User_Manual.pdf
AS-Quant example data for mouse(mouse mm10) is included in the folder https://github.com/compbiolabucf/AS-Quant/tree/main/sample_input_mouse. To run from scratch, users can use the sample data for quantization of AS events.
Please use the following information to cite.
MDPI and ACS Style Fahmi, N.A.; Nassereddeen, H.; Chang, J.; Park, M.; Yeh, H.; Sun, J.; Fan, D.; Yong, J.; Zhang, W. AS-Quant: Detection and Visualization of Alternative Splicing Events with RNA-seq Data. Int. J. Mol. Sci. 2021, 22, 4468. https://doi.org/10.3390/ijms22094468
AMA Style Fahmi NA, Nassereddeen H, Chang J, Park M, Yeh H, Sun J, Fan D, Yong J, Zhang W. AS-Quant: Detection and Visualization of Alternative Splicing Events with RNA-seq Data. International Journal of Molecular Sciences. 2021; 22(9):4468. https://doi.org/10.3390/ijms22094468
Chicago/Turabian Style Fahmi, Naima Ahmed, Heba Nassereddeen, Jaewoong Chang, Meeyeon Park, Hsinsung Yeh, Jiao Sun, Deliang Fan, Jeongsik Yong, and Wei Zhang. 2021. "AS-Quant: Detection and Visualization of Alternative Splicing Events with RNA-seq Data" International Journal of Molecular Sciences 22, no. 9: 4468. https://doi.org/10.3390/ijms22094468
Naima Ahmed Fahmi: [email protected] Wei Zhang: [email protected]