MAJEC: unified gene, isoform, and locus-level transposable element quantification from RNA-seq.

MAJEC achieves over 80% reduction in exon-overlap contamination for transposable element quantification from RNA-seq data, outperforming existing tools in locus-level accuracy.

• Why it matters: Accurate measurement of transposable elements (TEs) is vital for understanding their roles in diseases like cancer and processes such as aging, but current methods struggle with overlapping gene signals, limiting reliability.
• What they did: MAJEC employs a unified EM framework that jointly quantifies genes, isoforms, and TE loci from BAM alignments, integrating splice junction evidence to distinguish genic from TE-derived reads in a single pass.
• The result: This approach significantly reduces exon-overlap contamination, maintains high subfamily-level accuracy, and correctly resolves artifacts in TE activity, enabling more precise TE analysis in biological research.