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Prediction of variant Effect on Percent Spliced In
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README.md

PEPSI

Prediction of variant Effect on Percent Spliced In

https://github.com/rwang916/PEPSI

Authors: Robert Wang, Yaqiong Wang, Zhiqiang Hu

PEPSI is a tool created for predicting the impact of coding and noncoding variation on pre-mRNA splicing based on sequence conservation, RNA secondary structure, and regulatory sequence elements.

Please contact Robert Wang for feedback, questions, or bugs.

Table of Contents

Requirements

python

PEPSI requires python2 (>= 2.7.9)

R

PEPSI requires R (>= 3.2.2) and it is available on the R website.

Additional R packages needed are:

  • withr
  • ggplot2
  • randomForest
  • dplyr

parallel

GNU parallel is available on their website. The latest version of GNU parallel should be downloaded and installed. Make sure that the path to the 'parallel' executable is included in your 'PATH' environment variable.

tabix

tabix can be downloaded from their website. Follow the installation guidelines on their page. The latest version of tabix should be downloaded and installed. Have the path to the 'tabix' executable in your 'PATH' environment variable.

RNAplfold

RNAplfold is part of the ViennaRNA suite, which can be downloaded from their website. Download the latest release of the ViennaRNA suite and follow the instructions for installation. Include path to RNAplfold executable in your 'PATH' environment variable.

Installation

PEPSI can be downloaded (cloned) using the git command.

git clone https://github.com/rwang916/PEPSI.git

Once downloaded, run the following commands to download necessary files for running PEPSI

cd PEPSI/src
bash vs_build.sh

Usage

To run PEPSI, run:

bash vs_main.sh <path_to_training_set> <path_to_test_set> <number_of_threads> <path_to_training_set_sequences> <path_to_test_set_sequences>

Example usage:

bash vs_main.sh ../data/vexseq/HepG2_delta_PSI_CAGI_training.tsv ../data/vexseq/HepG2_delta_PSI_CAGI_test.tsv 20 
	../data/vexseq/vs.sequences.tsv ../data/vexseq/vs.sequences.tsv
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