majiq_splicing_analysis_pipeline

Introduction

ZarnackGroup/majiq_splicing_analysis_pipeline is a bioinformatics pipeline that ...

Our in-house pipeline for analyzing alternative splicing events from RNA sequencing data, based on Nextflow and utilizing MAJIQ as the core splicing analysis tool.

1. Read QC (FastQC)

2. Present QC for raw reads (MultiQC)

Usage

Note

If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

Now, you can run the pipeline using:

nextflow run ZarnackGroup/majiq_splicing_analysis_pipeline \
   -profile <docker/singularity/.../institute> \
   --input samplesheet.csv \
   --outdir <OUTDIR>

Warning

Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

Credits

majiq_splicing_analysis_pipeline was originally written by Felix Haidle.

We thank the following people for their extensive assistance in the development of this pipeline:

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

Citations

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.