Bioinformatics of simultaneous, quantitative measurements of full-length tRNA and tRNA fragments by MSR sequencing

tRNA fragments (tRFs) are generated by cellular endogenous ribonuclease cleavage and play important roles in cellular processes and diseases states. Many questions regarding tRF functions remain to be studied and understood. Common sequencing techniques measure tRF after a size selection step that separates the full-length tRNA and tRF before sequencing library construction. The crucial information on the relationship of tRFs to their respective full-length tRNA in the same biological sample cannot be obtained in this way. We developed multiplex small RNA sequencing (MSR-seq) which measures the abundance as well as site-specific modification information on both full-length tRNA and their matching tRFs in the same sample. Here we describe the bioinformatic steps to obtain the tRF abundance data from the MSR-seq data using the publicly available pipeline in Github (https://github.com/Luke-F1875/MSRseq_data_processing_pipeline).