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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 |
SAMTools and BEDTools
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mkdir -p $SCRATCH/core_ngs/samtools
cd $SCRATCH/core_ngs/samtools
cp $CORENGS/catchup/for_samtools/* . |