Quantifying uniformity of mapped reads

Abstract

We describe a tool for quantifying the uniformity of mapped reads in high-throughput sequencing experiments. Our statistic directly measures the uniformity of both read position and fragment length, and we explain how to compute a P-value that can be used to quantify biases arising from experimental protocols and mapping procedures. Our method is useful for comparing different protocols in experiments such as RNA-Seq. © The Author 2012. Published by Oxford University Press. All rights reserved.