Fig. 2

Schematic of tDRmapper. The input into tDRmapper is trimmed small RNA-seq reads. (Step 1) Reads are discarded if quality <28 at any position, length <14 or >41, or if the sequence does not occur >100 times in the FASTQ file. (Step 2) Reads are aligned according to a specific “error type hierarchy.” First reads are aligned, allowing for exact matches only to mature tRNA sequences, then reads that do not map are aligned allowing for exact matches to pre-tRNA sequences, and then reads that do not map are aligned allowing for one mismatch, then one deletion, two mismatches, two deletions, and then a three base pair deletion to mature tRNA sequences. (Step 3) tDRs are annotated based on size and location within either pre-tRNA or mature tRNA. (Step 4) tDRs are quantified based on two features, the fraction of reads aligning to the parent tRNA and the maximum coverage across all positions of the tRNA. (Step 5) tDRs are visualized as color-coded coverage maps