tsRNAsearch

tsRNAsearch leverages Nextflow DSL2 to identify, quantify, and rank tRNA fragments (tRFs) and other non-coding RNAs from small RNA-sequencing datasets for comparative analysis and biomarker discovery.

Key Features:

• Identification and quantification of ncRNAs: Detects and quantifies tRNA fragments (tRFs) and other non-coding RNAs in small RNA-seq data.
• Nextflow DSL2 workflow: Implements processing and comparative analyses using Nextflow DSL2.
• Handling sequence redundancy and short lengths: Addresses tRNA sequence redundancy and the short lengths of tRNAs/tRFs that complicate detection in sequencing data.
• Comparative analysis across experimental groups: Compares control and treatment groups to detect ncRNAs with irregular read distribution profiles indicative of RNA cleavage events.
• Innovative scoring system: Applies a combined score derived from four novel methods to rank tRNA fragments and other ncRNAs for differential abundance.

Scientific Applications:

• Disease Biomarker Discovery: Applied to small RNA-seq datasets from chronic hepatitis-infected liver tissue and pancreatic ductal adenocarcinoma (PDAC), reproducing known tRFs and highlighting miR135b and other miRNA candidates as potential biomarkers.
• Research in RNA Biology: Enables investigation of tRF biogenesis and functional roles by identifying cleavage-associated read distribution patterns and differentially abundant ncRNA species.

Methodology:

Implemented as a Nextflow DSL2 pipeline that performs a comparative differential expression analysis to search for tRNAs and other ncRNAs with irregular read distribution profiles indicative of cleavage events and uses a novel combined score from four methods to rank candidate ncRNAs.