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CapTrap-seq: a platform-agnostic and quantitative approach for high-fidelity full-length RNA sequencing.

Sílvia Carbonell-Sala¹, Tamara Perteghella^1,2, Julien Lagarde^1,3

¹Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain.

Nature Communications

|June 27, 2024

Summary

CapTrap-seq is a new method for preparing RNA for long-read sequencing. It accurately identifies full-length RNA transcripts, improving genome annotation across different sequencing platforms.

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Genome-wide Surveillance of Transcription Errors in Eukaryotic Organisms

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Published on: September 13, 2018

Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Accurate eukaryotic genome annotation relies on long-read RNA sequencing.
Identifying full-length RNA transcripts remains challenging for current long-read methods.

Purpose of the Study:

To develop and evaluate CapTrap-seq, a novel cDNA library preparation method.
To assess CapTrap-seq's performance in detecting 5' capped, full-length transcripts.

Main Methods:

CapTrap-seq combines Cap-trapping with oligo(dT) priming.
Evaluated CapTrap-seq against other RNA-seq protocols using human and mouse tissues.
Utilized both Oxford Nanopore (ONT) and PacBio sequencing technologies.
Incorporated synthetic RNA spike-ins with a capping strategy for quantitative assessment.

Main Results:

CapTrap-seq demonstrates competitive performance compared to existing methods.
The method is platform-agnostic, suitable for both ONT and PacBio sequencing.
Validated using Long-read RNA-seq Genome Annotation Assessment Project (LRGASP) data.

Conclusions:

CapTrap-seq is an effective RNA library preparation method for generating full-length transcript sequences.
This method enhances the accuracy and completeness of eukaryotic genome annotation.