nfcore/cageseq repository overview

⁠Introduction

nf-core/cageseq is a bioinformatics analysis pipeline used for CAGE-seq sequencing data.

The pipeline takes raw demultiplexed fastq-files as input and includes steps for linker and artefact trimming (cutadapt⁠), rRNA removal (SortMeRNA⁠, alignment to a reference genome (STAR⁠ or bowtie1⁠) and CAGE tag counting and clustering (paraclu⁠). Additionally, several quality control steps (FastQC⁠, RSeQC⁠, MultiQC⁠) are included to allow for easy verification of the results after a run.

The pipeline is built using Nextflow⁠, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.

⁠Quick Start

1. Install nextflow⁠

2. Install either Docker⁠ or Singularity⁠ for full pipeline reproducibility (please only use Conda⁠ as a last resort; see docs⁠)

3. Download the pipeline and test it on a minimal dataset with a single command:

   nextflow run nf-core/cageseq -profile test,<docker/singularity/conda/institute>
   

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   Please check nf-core/configs⁠ to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use -profile <institute> in your command. This will enable either docker or singularity and set the appropriate execution settings for your local compute environment.

4. Start running your own analysis!

nextflow run nf-core/cageseq -profile <docker/singularity/conda/institute> --input '*_R1.fastq.gz' --aligner <'star'/'bowtie1'> --genome GRCh38

See usage docs⁠ for all of the available options when running the pipeline.

⁠Documentation

The nf-core/cageseq pipeline comes with documentation about the pipeline which you can read at https://nf-co.re/cageseq/usage⁠ and https://nf-co.re/cageseq/output⁠ or find in the docs/ directory⁠.

⁠Credits

nf-core/cageseq was originally written by Kevin Menden (@KevinMenden⁠) and Tristan Kast (@TrisKast⁠) and updated by Matthias Hörtenhuber (@mashehu⁠).

⁠Contributions and Support

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

For further information or help, don't hesitate to get in touch on the Slack #cageseq channel⁠ (you can join with this invite⁠).

⁠Citation

You can cite the nf-core publication as follows: