Introduction

nf-core/circrna is a bioinformatics pipeline to analyse total RNA sequencing data obtained from organisms with a reference genome and annotation. It takes a samplesheet and FASTQ files as input, performs quality control (QC), trimming, back-splice junction (BSJ) detection, annotation, quantification and miRNA target prediction of circular RNAs.

The pipeline is still under development, but the BSJ detection and quantification steps are already implemented and functional. The following features are planned to be implemented soon:

• Isoform-level circRNA detection and quantification
• circRNA-miRNA interaction analysis using SPONGE and spongEffects
• Improved downstream analyses

If you want to contribute, feel free to create an issue or pull request on the GitHub repository or join the Slack channel.

Pipeline summary

• Raw read QC (FastQC)
• Adapter trimming (Trim Galore!)
• BSJ detection
  • CIRIquant
  • STAR 2-Pass mode
    • CIRCexplorer2
    • circRNA finder
    • DCC
  • find circ
  • MapSplice
  • Segemehl
• circRNA annotation
  • Based on a GTF file
  • Based on database files (if provided)
• Extract circRNA sequences and build circular transcriptome
• Merge circular transcriptome with linear transcriptome derived from provided GTF
• Quantification of combined circular and linear transcriptome
  • psirc-quant
• miRNA binding affinity analysis (only if the mature parameter is provided)
  • Normalizes miRNA expression (only if the mirna_expression parameter is provided)
  • Binding site prediction
    • miRanda
    • TargetScan
  • Perform majority vote on binding sites
  • Compute correlations between miRNA and transcript expression levels (only if the mirna_expression parameter is provided)
• Statistical tests (only if the phenotype parameter is provided)
  • CircTest
• MultiQC report 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.

nf-core/circrna: a portable workflow for the quantification, miRNA target prediction and differential expression analysis of circular RNAs.

Barry Digby, Stephen P. Finn, & Pilib Ó Broin

BMC Bioinformatics 24, 27 (2023) doi: 10.1186/s12859-022-05125-8

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

You can cite the nf-core publication as follows:

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.