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Even though many mapping tools exist, a few individual programs have a dominant "market share" of the NGS world. In this section, we will primarily focus on two of the most versatile mappers: BWA and Bowtie2, the latter being part of the Tuxedo suite which includes the transcriptome-aware RNA-seq aligner Tophat2 as well as other downstream quantifiaction tools.
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Stage the alignment data
First connect to login5.ls5.tacc.utexas.edu
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. This should be second nature by now 
Stage the alignment data
First Then stage the sample datasets and references we will use.
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