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).
Start by cloning MicroExonator
git clone https://github.com/hemberg-lab/MicroExonatorInstall 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.shFinally, create an enviroment to run snakemake
conda create -n snakemake_env -c bioconda -c conda-forge snakemakeExtended documentation can be found at https://microexonator.readthedocs.io.
For questions, ideas, feature requests and potential bug reports please contact geparada@utoronto.ca