Quantifying uniformity of mapped reads

Details Quantifying uniformity of mapped reads Quantifying uniformity of mapped reads

2011-09-26

arxiv.org/abs/1109.5681v1

Biology

Quantitative Biology

Genomics

Scientific paper

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 freely available and open source R code that can be used to analyze mapped reads in SAM format at http://bio.math.berkeley.edu/spRead/ Contact: lpachter@math.berkeley.edu

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