Leoberium / pyIPSA

Integrative Pipeline for Splicing Analysis

pyIPSA

Integrative Pipeline for Splicing Analysis

Installation & Run

To use this program you must have python environment with the following programs and libraries installed:

• snakemake
• pysam
• pandas
• numpy

Such environment may be created via conda:

1. conda create -n ipsa
2. conda activate ipsa
3. conda install -c conda-forge -c bioconda snakemake pysam pandas

To install the pipeline:
git clone https://github.com/Leoberium/pyIPSA.git

To run (test run if input directory is empty):

1. Python environment with required libraries must be active
2. Make directory with Snakefile active
3. Run snakemake command

Test run produces empty aggregated_junction_stats.tsv file in output directory.

Options for snakemake command are available in snakemake documentation.

For Arcuda users

Just load module with Python and install libraries:

1. module load ScriptLang/python/3.8.3
2. pip3 install --user --upgrade snakemake pandas pysam

After that you can run pipeline using cluster engine: snakemake --cluster qsub --j <number of jobs>

Working folders

Folder in repository:

1. config - the folder with config file, where you set up your pipeline
2. deprecated - the folder with old scripts not used in workflow
3. known_SJ - the folder with annotated splice junctions
4. workflow - the folder with working scripts of the pipeline

Additional directories created

1. genomes - the folder which stores all downloaded genomes
2. annotations - the folder which stores all downloaded annotations