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changes.mady.by.user Anna M Battenhouse

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changes.mady.by.user Anna M Battenhouse

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Code Block
languagebash
# 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

Anchor
Catchup_samtools
Catchup_samtools
Setup for samtools

Code Block
languagebash
titleSetup for samtools exercises
mkdir -p $SCRATCH/core_ngs/samtools
cd $SCRATCH/core_ngs/samtools
cp $CORENGS/catchup/for_samtools/* .