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).

Contents:

• Installation
  • Initialize a project
  • Other DROP versions
  • Installation without conda
• Preparing the Input Data
  • Config file
  • Modularization of DROP
  • Creating the sample annotation table
  • Limiting FDR correction to subsets of genes of interest
  • Files to download
  • Example of RNA replicates
  • Advanced options
• Pipeline Commands
  • Dry run
  • Parallelizing jobs
  • Executing subworkflows
  • Rerunning the pipeline
• Results and Output of DROP
  • Aberrant Expression
  • Aberrant Splicing
  • Mono-allelic Expression
  • RNA Variant Calling
• License

Quickstart

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.