DROP - Detection of RNA Outliers Pipeline¶
DROP is intended to help researchers use RNA-Seq data in order to detect genes with aberrant expression, aberrant splicing, mono-allelic expression, and RNA-Seq variant calling. It consists of 4 independent modules for each of those strategies. After installing DROP, the user needs to fill in the config file and sample annotation table (Preparing the Input Data). Then, DROP can be executed in multiple ways (Pipeline Commands).
- Preparing the Input Data
- Pipeline Commands
- Results and Output of DROP
DROP is available on bioconda. We recommend using a dedicated conda environment. (installation time: ~ 10min) Use mamba instead of conda as it provides more reliable and faster dependency solving.
mamba create -n drop -c conda-forge -c bioconda drop
Test installation with demo project
mkdir ~/drop_demo cd ~/drop_demo drop demo
The pipeline can be run using snakemake commands
snakemake --cores 1 -n # dryrun snakemake --cores 1
Expected runtime: 25 min
For more information on different installation options, refer to Installation.