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Thus, a large set of computational tools have been developed to quickly, and with sufficient (but NOT absolute) accuracy align each read to its best location, if any, in a reference. Even though many mapping tools exist, a few individual programs have a dominant "market share" of the NGS world. These programs vary widely in their design, inputinputs, outputoutputs, and applicabilityapplicationsIn this section, we will primarily focus on two of the most versatile mappers: BWA and Bowtie2, the latter being part of the Tuxedo suite (e.g. Tophat2).

Theoretical Background and Possible Cases

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Sample Datasets

You have already worked with one paired-end yeast ChIP-seq dataset, which we will continue to use here.  In order to demonstrate how to process 

Reference Genomes

 

BWA - The Most General Mapper

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