title: 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.
  
  
  METHODS
  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.
authors: Department of Mathematics, University of Miami, Coral Gables, FL 33146, USA.
authors: Valerie
authors: V
authors: Hower
authors: Richard
authors: R
authors: Starfield
authors: Adam
authors: A
authors: Roberts
authors: Lior
authors: L
authors: Pachter
mesh_terms: D003627:Data Interpretation, Statistical; D059014:High-Throughput Nucleotide Sequencing / Q000592:standards*; D011786:Quality Control; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA / Q000592:standards; D012984:Software