rMATS-turbo-tutorial

Source code and input files related to the figures in the rMATS-turbo manuscript "rMATS-turbo: an efficient and flexible computational tool for alternative splicing analysis of large-scale RNA-seq data"

Figure 2

• The static HTML format of figure generating process is demonstrated in plot_Fig_PC3E_GS689.html
• Source code for generating Figure 2 is demonstrated in plot_Fig_PC3E_GS689.ipynb
• Input files for generating Figure 2 is located in folder PC3E-GS689
• The output files are created in ./PC3E-GS689/plot_rmats2sashimi/output/Sashimi_plot/ and ./PC3E-GS689/plot_venn_volcano

Figure 3

• The static HTML format of figure generating process is demonstrated in plot_Fig_CCLE.html
• Source code for generating Figure 3 is demonstrated in plot_Fig_CCLE.ipynb
• Input files for generating Figure 3 is located in folder CCLE
• The output file is ./CCLE/plot_heatmap/plot_heatmap_sortedByEMT_usingCorrelation.pdf

Requirements

• Jupyter Notebook
• rmats2sashimiplot
• Python related dependencies:
  • rpy2
• R packages
  • zeallot
  • ComplexHeatmap
  • circlize
  • ggplot2
  • ggrepel
• GNU sed

Install

• MAC users: install GNU sed
  • brew install gnu-sed
  • PATH="/usr/local/opt/gnu-sed/libexec/gnubin:$PATH"
• install most dependencies to a conda environment
  • conda create --prefix ./conda_env
  • conda activate ./conda_env
  • conda install -c conda-forge -c bioconda --file ./conda_requirements.txt
  • CFLAGS="-I$(pwd)/conda_env/include" pip install rpy2==2.8.6
  • conda deactivate
• install rmats2sashimiplot and samtools
  • conda install -c conda-forge -c bioconda --file ./conda_requirements_rmats2sashimiplot.txt

Run

• Activate the main conda_env
  • conda activate ./conda_env
• The code in plot_Fig_PC3E_GS689.ipynb and plot_Fig_CCLE.ipynb can be run interactively in web browser via Jupyter Notebook.
  • Launching Jupyter Notebook
    • jupyter notebook
• It can also be run as an entire script
  • Convert notebooks to scripts
    • jupyter nbconvert --to python ./plot_Fig_PC3E_GS689.ipynb
    • jupyter nbconvert --to python ./plot_Fig_CCLE.ipynb
  • For the PC3E notebook:
    • ipython ./plot_Fig_PC3E_GS689.py
  • For the CCLE notebook:
    • ipython ./plot_Fig_CCLE.py