ROP

Read Origin Protocol (ROP) assigns origins to mapped and unmapped RNA-seq reads to characterize complex RNA molecules and transcriptomic components.

Key Features:

• Comprehensive Read Origin Assignment: Identifies sources of mapped and unmapped RNA-seq reads, enabling characterization of diverse RNA species and previously unannotated transcripts.
• Large-Scale Processing Capability: Processes up to one trillion reads and accounts for 99.9% of reads across datasets spanning 2630 individuals and 54 human tissues.

Scientific Applications:

• Transcriptomic Complexity and Host–Microbiome Analysis: Supports discovery of novel transcripts, alternative splicing events, and interactions linking the immune system, microbiome, and disease states.

Methodology:

ROP implements a multi-step RNA-seq analysis pipeline that systematically reanalyzes unmapped and mapped reads using sequential alignment and classification strategies to assign read origins and maximize transcriptome coverage.