SPLICE-q

A Python tool for genome-wide SPLIcing Efficiency quantification from RNA-seq data.

User Manual

Features

• Quantification of individual intron splicing efficiencies from strand-specific RNA-seq data.
• Sensitive to the overlap of genomic elements.
• Fast and user-friendly.

Installation

SPLICE-q can be installed from pip and from source.

pip

Using pip is the easiest way to install SPLICE-q.

 $ pip install SPLICE-q

Development/install from source

 $ git clone https://github.com/vrmelo/SPLICE-q
 $ cd SPLICE-q
 $ pip install -e .

Requirements

• Python 3.6+
• PySam
• InterLap
• NumPy
• Rich

Operating Systems

• Linux, macOS, and Windows 10 Subsystem for Linux.

Usage

To run SPLICE-q with default parameters, it requires a BAM file and a genome annotation file provided by GENCODE or Ensembl (GTF):

$ SPLICE-q.py -b file.bam -g annotation.gtf

To specify an output file name and location:

$ SPLICE-q.py -b file.bam -g annotation.gtf -o outfile.tsv

Need help?

$ SPLICE-q.py -h

or check our User Manual.

Citation

de Melo Costa, Verônica R., et al. "SPLICE-q: a Python tool for genome-wide quantification of splicing efficiency." BMC bioinformatics 22.1 (2021): 1-14.