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Related Experiment Video

Updated: Jan 23, 2026

Identification of Coding and Non-coding RNA Classes Expressed in Swine Whole Blood

Identification of Coding and Non-coding RNA Classes Expressed in Swine Whole Blood

Published on: November 28, 2018

CRESCENT, a comprehensive RNA-Seq expression, splicing, and coding/non-coding element network tool.

Gilles Sireta¹, Gwendal Cueff², Vincent Darbot³

¹Université Clermont Auvergne, CNRS, INSERM, iGReD Clermont-Ferrand, Clermont-Ferrand, France.

BMC Bioinformatics

|January 21, 2026

Summary

This summary is machine-generated.

This study introduces CRESCENT, a comprehensive RNA-Seq analysis tool that integrates coding and non-coding elements, splicing, and transcript usage. CRESCENT provides a scalable solution for detailed transcriptomic profiling across diverse species and computational environments.

Keywords:

Alternative splicing Non-coding RNA Protein coding genes RNA-Seq workflow Snakemake Transposable elements

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Last Updated: Jan 23, 2026

Identification of Coding and Non-coding RNA Classes Expressed in Swine Whole Blood

Identification of Coding and Non-coding RNA Classes Expressed in Swine Whole Blood

Published on: November 28, 2018

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

RNA Pull-down Procedure to Identify RNA Targets of a Long Non-coding RNA

RNA Pull-down Procedure to Identify RNA Targets of a Long Non-coding RNA

Published on: April 10, 2018

Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

Traditional RNA-Seq analysis often overlooks non-coding elements like transposable elements (TEs) and non-coding RNA.
Limited analysis of splicing events and transcript usage hinders a complete understanding of transcriptomic regulation.
A comprehensive approach is needed to capture the full complexity of the transcriptome.

Purpose of the Study:

To develop an automated and comprehensive RNA-Seq analysis workflow.
To integrate the analysis of differential expression, splicing, and transcript usage for both coding and non-coding elements.
To provide a user-friendly and scalable solution for transcriptomic profiling.

Main Methods:

Developed CRESCENT (Comprehensive RNA-seq Expression, Splicing, and Coding/non-coding Element Network Tool), a Snakemake workflow.
Integrated multiple bioinformatic tools and Snakemake wrappers for streamlined analysis.
Validated the workflow using existing datasets and benchmarked performance on various computational platforms.

Main Results:

CRESCENT enables automated analysis of differential expression, alternative splicing, and transcript usage.
Validated results for protein-coding genes, TEs, and alternative splicing align with previous findings.
The workflow is scalable, running on personal computers to high-performance computing clusters for diverse sequencing data and species.

Conclusions:

CRESCENT offers a scalable and comprehensive solution for transcriptomic profiling.
The tool facilitates a more nuanced understanding of expression dynamics by integrating diverse genomic elements.
CRESCENT is freely available, promoting broader accessibility for transcriptomic research.