txtools: an R package facilitating analysis of RNA modifications, structures, and interactions

Area of Science:

• Bioinformatics
• Genomics
• Molecular Biology

Background:

• RNA sequencing (RNA-seq) is crucial for understanding gene expression.
• Analyzing RNA-seq data at nucleotide resolution presents computational challenges.
• Existing tools may not fully integrate genomic alignments with transcriptomic representations.

Purpose of the Study:

• To introduce txtools, an R package designed for detailed nucleotide-level RNA-seq analysis.
• To provide a user-friendly framework for processing, analyzing, and visualizing RNA-seq data.
• To facilitate discoveries in epitranscriptomics and related fields.

Main Methods:

• Input: BAM files (aligned sequencing reads) and transcriptome annotations.
• Processing: Nucleotide-level analysis of mismatches, deletions, and read start/end positions.
• Output: A comprehensive table summarizing transcriptomic events at each nucleotide.

Main Results:

• txtools enables seamless integration of genomic alignments with transcriptomic data.
• The package generates detailed nucleotide-level information, including mismatches and read coverage.
• Demonstrated utility in epitranscriptomics, yielding insightful and publishable results with minimal function calls.

Conclusions:

• txtools offers a powerful and intuitive R package for advanced RNA-seq analysis.
• The tool is valuable for epitranscriptomics, structural mapping, and RNA:protein interaction studies.
• txtools simplifies complex analyses, potentially accelerating future discoveries in RNA biology.