PredPSI-SVR

PredPSI-SVR was designed to predict the change of percent spliced in (delta-PSI or ) caused by genetic variants for the CAGI 5 vex-seq challenge.

• About and : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3037023/

Send questions and comments to chenkenbio@gmail.com

Requirements

• Operation system: Unix/Linux
• Memory: 4GB at least
• Perl in your PATH
• Python 2
• Python 3 (with numpy package installed)
  If you have trouble installing python 3 or numpy, you can try miniconda

  cd ~/Downloads
  wget -c https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
  chmod +x Miniconda3-latest-Linux-x86_64.sh
  ./Miniconda3-latest-Linux-x86_64.sh             #pay attention to path of installation, we'll use the default path "$HOME/miniconda3" in this tutorial 
  source $HOME/miniconda/bin/activate
  pip install numpy

Getting started

Preparation

Note: If you have the following packages installed on your system, you can skip installing them and just edit path in src/init.sh
We put PrePSI-SVR in $HOME directory as default

1. Download PredPSI-SVR,

   cd ~
   git clone https://github.com/chenkenbio/PredPSI-SVR

2. Download ANNOVAR (http://annovar.openbioinformatics.org/en/latest/user-guide/download/), libsvm (https://www.csie.ntu.edu.tw/~cjlin/libsvm), and samtools (http://www.htslib.org/download/). And move them to PredPSI-SVR/tools.

3. Extract packages:

   cd ~/PredPSI-SVR/tools
   tar -xzvf annovar.latest.tar.gz
   tar -xzvf libsvm-3.23.tar.gz
   tar -xjvf samtools-1.9.tar.bz2
   cd libsvm-3.23
   make all
   cd ../samtools-1.9
   make all
   cd ..

4. Download basic annotation databases for ANNOVAR

   cd ~/PredPSI-SVR/tools/annovar        # PredPSI-SVR/tools
   ./annotate_variation.pl -buildver hg19 -downdb -webfrom annovar ensGene ./humandb/

5. Download third-party database SPIDEX from http://www.openbioinformatics.org/annovar/spidex_download_form.php. Move it to ~/PredPSI-SVR/tools/annovar/humandb/ and decompress with unzip:

unzip hg19_spidex.zip        #working directory: PredPSI-SVR/tools/annovar/humandb

6. Download hg19 genome

cd ~/PredPSI-SVR/genome
wget -c http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz
cat *.fa > hg19.fasta
$HOME/PredPSI-SVR/tools/samtools-1.9/samtools faidx hg19.fasta

7. Finally, check variables in src/init.sh, edit them to fit your system

Usage

Example:

cd ~/PredPSI-SVR/
## PredPSI-SVR, with "-p" option
./main.sh example/sample.vcf -p example/sample.psi -o example/outdir
## PredPSI-SVR-noPSI, with out "-p"
./main.sh example/sample.vcf -o example/outdir

Result file is example/outdir/OUTPUT.dpsi

Attention:

The PredPSI-SVR will filter the VCF file at first to remove variants in intergenic regions or distant to splice sites (more than 200 bp ). Threrefore sometimes you will find that there are fewer variants in OUTPUT.psi than your input VCF file.

References

PredPSI-SVR/tools/ese3/ese3_mod.py is modified based a script in SilVA package (Paper: https://www.ncbi.nlm.nih.gov/pubmed/23736532, GitHub: https://github.com/buske/silva)

Citation

Chen, K., Lu, Y., Zhao, H., & Yang, Y. (2019). Predicting the change of exon splicing caused by genetic variant using support vector regression. Human mutation, 40(9), 1235–1242. https://doi.org/10.1002/humu.23785