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changes.mady.by.user Anna M Battenhouse

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Anchor
Catchup_references
Catchup_references
References

Get a copy of all references we build in the exercises (including FASTA):

Code Block
languagebash
mkdir -p $SCRATCH/core_ngs/references
rsync -ptlvrP $CORENGS/references/ $SCRATCH/core_ngs/references/

Anchor
Catchup_bwa_pe_yeast
Catchup_bwa_pe_yeast
BWA PE alignment of yeast data

To jump into aligning PE yeast data with BWA

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