srnaMapper

srnaMapper maps short RNA sequencing reads to reference genomes to identify genomic origins of micro RNAs, tRNA-derived RNAs, and piwi-interacting RNAs while accounting for sRNA-specific properties such as short length, redundancy, duplicated loci, and end modifications.

Key Features:

• Optimized for Short Reads: Tailored to handle short RNAs including micro RNAs, tRNA-derived RNAs, and piwi-interacting RNAs with read lengths not exceeding 200 base pairs.
• Efficient Mapping with Error Handling: Leverages the bwa API and bwa index files to retrieve all potential hits while accommodating an arbitrary number of sequencing errors and end modifications.
• Redundancy and Duplicated Loci Handling: Manages sRNA redundancy and maps reads originating from duplicated loci to ensure comprehensive source identification.
• Performance: Demonstrates superior computation time relative to existing tools for large-scale sRNA datasets.

Scientific Applications:

• sRNA Impact Studies: Provides precise mapping to support investigation of functional roles and regulatory mechanisms of diverse short RNAs.
• Genomic Research: Enables exploration of genomic origins of sRNAs, including those from duplicated loci or subject to post-transcriptional modifications.

Methodology:

srnaMapper integrates with the bwa API and uses pre-generated bwa index files to align short RNA reads to reference genomes, retrieving all potential hits and allowing an arbitrary number of sequencing errors.