Quantifying uniformity of mapped reads.
Ontology highlight
ABSTRACT: Unlabelled
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.
SUBMITTER: Hower V
PROVIDER: S-EPMC3467739 | biostudies-literature | 2012 Oct
REPOSITORIES: biostudies-literature
Publications
Quantifying uniformity of mapped reads.
Hower Valerie V Starfield Richard R Roberts Adam A Pachter Lior L
Bioinformatics (Oxford, England) 20120718 20
<h4>Unlabelled</h4>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.<h4>Availability and implementation</h4>We provide a freely ...[more]
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