De novo vs resequencing sample preparaaon re

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Unformatted text preview: are using cs servers then you shouldn’t have to do this step. Export the path or use the exact path. ! ! ! ! ! ! ! ! !bunzip2 bwa-0.5.9.tar.bz2 ! !tar xvf bwa-0.5.9.tar! !cd bwa-0.5.9 | make! !make Download the reference genome using wget. Create the index for the reference genome (assuming the reference sequences are in wg.fa). Only needs to be performed once for each genome. Use –a for small genomes. ! !bwa index -p hg19bwaidx -a bwtsw wg.fa! Mapping short reads to the reference genome. 1. Align...
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