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Code Block
titleGet the alignment exercises files
mkdir -p $SCRATCH/core_ngs/alignment/fastq
mkdir -p $SCRATCH/core_ngs/references/fasta
cp $CORENGS/alignment/*fastq.gz $SCRATCH/core_ngs/alignment/fastq/
cp $CORENGS/references/*.*fa $SCRATCH/core_ngs/references/fasta/


We can quickly index the references for the yeast genome, the human miRNAs, and the V. cholerae genome, because they are all small, so we'll build each index from the appropriate FASTA files right before we use them. We will also obtain the special GenBank file that contains both the V. cholerae genome sequence and annotations (a .gbk file). These FASTA files, which you staged above, are: 

Code Block
titleReference FASTA locations

hg19 is way too big for us to index here so we will use an existing set of BWA hg19 index files located at: