peaks2utr

peaks2utr annotates 3' untranslated regions (3' UTRs) by leveraging UTR-enriched single-cell RNA sequencing data (e.g., 10× Chromium) to refine and extend transcript annotations in nonmodel organisms.

Key Features:

• UTR enrichment utilization: Leverages 3' UTR enrichment from single-cell RNA-seq (10× Chromium) to detect 3' UTR regions often missing from standard annotations.
• Input and output formats: Processes aligned sequencing reads in BAM format together with canonical annotations in GFF or GTF format and produces enhanced annotation files including extended 3' UTRs.
• Annotation refinement: Refines and extends existing transcript annotations by identifying and attributing enriched 3' UTR regions to genes.

Scientific Applications:

• 3' UTR annotation in nonmodel organisms: Complements incomplete or absent 3' UTR annotations to improve transcriptome annotation in nonmodel species.
• Post-transcriptional regulation studies: Enables analysis of mRNA stability, localization, and translation efficiency by providing more complete 3' UTR annotations.
• Single-cell transcriptomics interpretation: Improves interpretation of gene expression and transcript structure in single-cell RNA-seq datasets by supplying refined 3' UTR information.

Methodology:

Processes BAM files of aligned reads and canonical annotations in GFF/GTF formats, identifies regions enriched for 3' UTRs using UTR-enriched single-cell sequencing data, and outputs an enhanced annotation file with extended 3' UTRs.