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Code Block
languagebash
# Pre-built references
mkdir -p $SCRATCH/core_ngs/references
rsync -ptlvrPavrP $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

Anchor
Catchup_bwa_pe_yeast
Catchup_bwa_pe_yeast
samtools manipulation of aligned yeast data

To jump into post-alignment manipulation of the yeast_pairedend.bam with samtools:

Code Block
languagebash
mkdir -p $SCRATCH/core_ngs/alignment/yeast_bwa
cd $SCRATCH/core_ngs/alignment/yeast_bwa
cp $CORENGS/catchup/yeast_bwa/yeast_pairedend.bam .
module load samtools

# If the sorted, indexed BAM is needed:
cp $CORENGS/catchup/yeast_bwa/yeast_pairedend.sort* .

SAMTools and BEDTools

Anchor
Catchup_samtools
Catchup_samtools
Setup for samtools

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