tRNAstudio

tRNAstudio analyzes tRNA‑Seq datasets to quantify tRNA gene expression, classify reads as precursor or mature tRNAs, assess tRNA sequence coverage and post‑transcriptional modifications, and enable comparative analyses across samples.

Key Features:

• tRNA gene expression quantification: Quantifies tRNA gene expression and supports differential analysis using DESeq2 and Iso-tRNA-CP.
• Read classification: Classifies sequencing reads into precursor tRNAs (pre-tRNAs) and mature/processed tRNAs.
• tRNA gene sequence coverage: Computes sequence coverage across tRNA genes to evaluate read distribution and completeness.
• Post-transcriptional modification analysis: Assesses levels and patterns of post-transcriptional modifications in tRNAs.
• Analytical outputs: Produces graphical representations and numerical tables summarizing expression, coverage, classification, and modification analyses.

Scientific Applications:

• Validation across sample types: Validated on datasets generated from multiple experimental methods across human cell lines and tissues.
• tRNA pool dynamics: Characterizes dynamics of the cellular tRNA pool across conditions or timepoints.
• tRNA modification studies: Examines variations in tRNA post-transcriptional modifications and their potential regulatory roles.
• tRNA processing comparisons: Detects differences in tRNA processing between biological conditions or disease states.

Methodology:

Implements a mapping workflow tailored for small RNA-seq datasets (single-end and paired-end) and employs DESeq2 and Iso-tRNA-CP for expression analysis.