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Now, we're ready to execute the actual alignment, with the goal of initially producing a SAM file from the input FASTQ files and reference. First prepare a directory for this exercise and link the sacCer3 reference directories there (this will make our commands more readable).

Expand
titleSetup (if needed)
Code Block
languagebash
# Copy the pre-built references
mkdir -p $SCRATCH/core_ngs/references
rsync -avrP $CORENGS/references/ $SCRATCH/core_ngs/references/

# Get the FASTQ to align
mkdir -p $SCRATCH/core_ngs/alignment/fastq
cp $CORENGS/alignment/*fastq.gz $SCRATCH/core_ngs/alignment/fastq/
Code Block
languagebash
titlePrepare to align yeast data
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

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