hemberg-lab / MicroExonator

Snakemake pipeline for microexon discovery and quantification

Introduction

MicroExonator is a fully-integrated computational pipeline that allows for systematic de novo discovery and quantification of microexons using raw RNA-seq data for any organism with a gene annotation. Compared to other available methods MicroExonator is more sensitive for discovering smaller microexons and it provides higher specificity for all lengths. Moreover, MicroExonator provides integrated downstream comparative analysis between cell types or tissues using Whippet (Sterne-Weiler et al. 2018).

Installation

Start by cloning MicroExonator

git clone https://github.com/hemberg-lab/MicroExonator

Install Miniconda 3

wget 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

Finally, create an enviroment to run snakemake

conda create -n snakemake_env -c bioconda -c conda-forge snakemake

Documentation

Extended documentation can be found at https://microexonator.readthedocs.io.

Contact

For questions, ideas, feature requests and potential bug reports please contact [e-mail]