3t-seq: automatic gene expression analysis of single-copy genes, transposable elements, and tRNAs from RNA-seq data

Area of Science:

• Genomics
• Bioinformatics
• Molecular Biology

Background:

• RNA sequencing is standard for quantifying transcriptomic changes.
• Existing methods often overlook transcripts from repetitive sequences like transposable elements (TEs) and transfer RNAs (tRNAs).
• There is a need for integrated software to analyze diverse RNA types.

Purpose of the Study:

• To present 3t-seq, a Snakemake pipeline for integrated differential expression analysis.
• To enable analysis of transcripts from single-copy genes, TEs, and tRNAs within a single workflow.
• To provide accessible reports and user-friendly results from raw sequencing data.

Main Methods:

• Developed a Snakemake pipeline named 3t-seq.
• Integrated quality control, genome mapping, and gene expression quantification.
• Implemented three methods for TE quantification and one for tRNA gene quantification.

Main Results:

• 3t-seq performs integrated differential expression analysis for multiple RNA types.
• The pipeline generates accessible reports and easy-to-use results for downstream analysis.
• It simplifies the management of software dependencies for user convenience.

Conclusions:

• 3t-seq offers a comprehensive solution for analyzing diverse RNA transcripts.
• The pipeline facilitates the study of transposable elements and transfer RNAs alongside single-copy genes.
• It streamlines RNA sequencing data analysis, making complex transcriptomic studies more accessible.