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Working with some yeast ChIP-seq FASTQ data:

Code Block
languagebash
# AreaCreate fora "original"$SCRATCH sequencingarea datato mkdirwork -p $WORK2/archive/original/2018_05.core_ngs
cd $WORK2/archive/original/2018_05.core_ngs
wget http://web.corral.tacc.utexas.edu/BioITeam/yeast_stuff/Sample_Yeast_L005_R1.cat.fastq.gz
wget http://web.corral.tacc.utexas.edu/BioITeam/yeast_stuff/Sample_Yeast_L005_R2.cat.fastq.gz

# Create a $SCRATCH area for FASTQ prep and link the yeast data thereon data for this course,
# with a sub-direct[1ory for pre-processing raw fastq files
mkdir -p $SCRATCH/core_ngs/fastq_prep

# Make symbolic links to the original yeast data:
cd $SCRATCH/core_ngs/fastq_prep
ln -s -f $WORK/archive/original/2018_05.core_ngs$CORENGS/yeast_stuff/Sample_Yeast_L005_R1.cat.fastq.gz
ln -s -f $WORK/archive/original/2018_05.core_ngs$CORENGS/yeast_stuff/Sample_Yeast_L005_R2.cat.fastq.gz

# Copy over a small FASTQ file
cd $SCRATCH/core_ngs/fastq_prep
cp $CORENGS/misc/small.fq .

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