The mapping sensitivity vs. False Discovery Rate (FDR) curves under different mapping quality (mapQ) cutoffs for the simulated RNA-seq datasets.

<p>The mapQ varies from 0, 3, 6, 10, 13, 20, then in increments of 10 up to the maximum allowed values of the indicated aligner. “Default” indicates aligners’ default best hits; “AlignerBoost” indicates best hits via AlignerBoost mapping and filtering procedures. A: Single-end (SE) mapping; B: Paired-end (PE) mapping.