Analyzing, visualizing, and annotating tRNA-derived RNAs using tRAX and tDRnamer.

tRNA-derived RNAs (tDRs) are known for their diverse regulatory roles in many organisms. These small RNA transcripts have been identified mainly by high-throughput RNA sequencing, numbering hundreds to thousands of unique molecules in any given biological sample. As such, bioinformatic analysis is essential in understanding the features, complexity, and unexplored biological patterns of tDRs. This chapter describes use of tRAX: tRNA Analysis of eXpression, a specially designed comprehensive end-to-end software pipeline for tDR abundance estimation, differential expression comparison, and inference of RNA modifications from raw small RNA sequencing data. We also demonstrate tDRnamer, a web- and command-line-based companion tool that provides automated, standardized tDR naming and annotations based on source tRNAs and related tDRs.