  Summary: 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.
  Availability and Implementation: We provide a freely available and open
source python script that can be used to analyze raw read data or reads mapped
to transcripts in BAM format at http://www.math.miami.edu/~vhower/ReadSpy.html .
  Contact<EMAIL_ADDRESS>