🐕 shiba2sashimi 🍣 (v0.1.7)

A utility to create Sashimi plots, a publication-quality visualization of RNA-seq data, from Shiba output. Greatly inspired by rmats2sashimiplot and MISO‘s original implementation.

Quick start

shiba2sashimi -e /path/to/Shiba/experiment_table.tsv \
-s /path/to/Shiba/workdir/ -o img/sashimi_example.png \
--id "SE@chr2@157561213-157561293@157560260-157561542"

Sashimi plot example

How to install

pip

pip install shiba2sashimi

git clone https://github.com/Sika-Zheng-Lab/shiba2sashimi.git
cd shiba2sashimi
pip install .

conda

conda create -n shiba2sashimi -c bioconda -c conda-forge shiba2sashimi
conda activate shiba2sashimi

Docker

docker pull naotokubota/shiba2sashimi

Dependencies

python (>=3.9)
numpy (>=1.18.0,<2.0.0)
matplotlib (>=3.1.0)
pysam (>=0.22.0)

Usage

usage: shiba2sashimi [-h] -e EXPERIMENT -s SHIBA -o OUTPUT [--id ID] [-c COORDINATE] [--samples SAMPLES] [--groups GROUPS] [--colors COLORS] [--width WIDTH] [--extend_up EXTEND_UP] [--extend_down EXTEND_DOWN]
                     [--smoothing_window_size SMOOTHING_WINDOW_SIZE] [--font_family FONT_FAMILY] [--nolabel] [--nojunc] [--minimum_junc_reads MINIMUM_JUNC_READS] [--dpi DPI] [-v]

shiba2sashimi v0.1.7 - Create Sashimi plot from Shiba output

optional arguments:
  -h, --help            show this help message and exit
  -e EXPERIMENT, --experiment EXPERIMENT
                        Experiment table used for Shiba
  -s SHIBA, --shiba SHIBA
                        Shiba working directory
  -o OUTPUT, --output OUTPUT
                        Output file
  --id ID               Positional ID (pos_id) of the event to plot
  -c COORDINATE, --coordinate COORDINATE
                        Coordinates of the region to plot
  --samples SAMPLES     Samples to plot. e.g. sample1,sample2,sample3 Default: all samples in the experiment table
  --groups GROUPS       Groups to plot. e.g. group1,group2,group3 Default: all groups in the experiment table. Overrides --samples
  --colors COLORS       Colors for each group. e.g. red,orange,blue
  --width WIDTH         Width of the output figure. Default: 8
  --extend_up EXTEND_UP
                        Extend the plot upstream. Only used when not providing coordinates. Default: 500
  --extend_down EXTEND_DOWN
                        Extend the plot downstream. Only used when not providing coordinates. Default: 500
  --smoothing_window_size SMOOTHING_WINDOW_SIZE
                        Window size for median filter to smooth coverage plot. Greater value gives smoother plot. Default: 21
  --font_family FONT_FAMILY
                        Font family for labels
  --nolabel             Do not add sample labels and PSI values to the plot
  --nojunc              Do not plot junction arcs and junction read counts to the plot
  --minimum_junc_reads MINIMUM_JUNC_READS
                        Minimum number of reads to plot a junction arc. Default: 1
  --dpi DPI             DPI of the output figure. Default: 300
  -v, --verbose         Increase verbosity

Contributing

Thank you for wanting to improve shiba2sashimi! If you have any bugs or questions, feel free to open an issue or pull request.

Citation

If you use shiba2sashimi in your research, please cite the original Shiba paper:

Kubota N, Chen L, Zheng S. Shiba: a versatile computational method for systematic identification of differential RNA splicing across platforms. Nucleic Acids Research 53(4), 2025, gkaf098.

Authors

Naoto Kubota (0000-0003-0612-2300)
Liang Chen (0000-0001-6164-4553)
Sika Zheng (0000-0002-0573-4981)