Titlebook: Statistical Genomics; Methods and Protocol Ewy Mathé,Sean Davis Book 2016 Springer Science+Business Media New York 2016 sequence data forma

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Book 2016tions, and representative tools for operating on genomic data. .Statistical Genomics: Methods and Protocols .is divided into four sections. The first section discusses overview material and resources that can be applied across topics mentioned throughout the book. The second section covers prominent

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Quantitative Comparison of Large-Scale DNA Enrichment Sequencing Datasidering variation across replicates. The protocol provides a detailed description for the comparative analysis of DNA-IP sequencing data including basic data processing, quality controls, and identification of differential enrichment using the Bioconductor package “MEDIPS”.

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Variant Calling From Next Generation Sequence Dataayes or bam2mpg software. ANNOVAR is then used to annotate the predicted variants using gene models, population frequencies, and predicted mutation severity, producing variant files which can be viewed and filtered with the variant display tool VarSifter.

APO

Operating on Genomic Ranges Using BEDOPSficient in both memory and time by chaining together combinations of its complementary components. The principal utilities accept raw or compressed data in a flexible format, and they provide built-in features to expedite parallel computations.

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Study Design for Sequencing Studiesand more to address molecular biology questions. By applying principles of statistical experimental design, sequencing experiments can be made more sensitive to the effects under study as well as more biologically sound, hence more replicable.

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