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Now, try aligning it with bwa aln like we did in Example #1, but first link to the hg19 bwa index directory.

Code Block
languagebash
titleLink to BWA hg19 index directory
cd $SCRATCH/core_ngs_align
ln -s -f /scratch/01063/abattenh/ref_genome/bwa/bwtsw/hg19
ls hg19

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