%0 Journal Article
%T Quantifying uniformity of mapped reads
%A Valerie Hower
%A Richard Starfield
%A Adam Roberts
%A Lior Pachter
%J Quantitative Biology
%D 2011
%I arXiv
%X 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: lpachter@math.berkeley.edu
%U http://arxiv.org/abs/1109.5681v3