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# Pre-built references
mkdir -p $SCRATCH/core_ngs/references
rsync -ptlvrP $CORENGS/references/ $SCRATCH/core_ngs/references/
# FASTQ (to align)
mkdir -p $SCRATCH/core_ngs/alignment/fastq
cp $CORENGS/alignment/*fastq.gz $SCRATCH/core_ngs/alignment/fastq/
# Alignment directory
mkdir -p $SCRATCH/core_ngs/alignment/yeast_bwa
cd $SCRATCH/core_ngs/alignment/yeast_bwa
ln -s -f ../fastq
ln -s -f ../../references/bwa/sacCer3
module load bwa
module load samtools |
SAMTools and BEDTools
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mkdir -p $SCRATCH/core_ngs/samtools
cd $SCRATCH/core_ngs/samtools
cp $CORENGS/catchup/for_samtools/* .
module load samtools |