2-ii. Quality control of sequence data

Copy the subsetted FASTQ files to your directory:

cd $TELE_ANALYSIS_DIR

cat samples.txt | while read samp; do
    mkdir -p $samp
    ln -fs /groups/nixonlab/telescope_tutorial.git/analysis/$samp/${samp}_pass_1.fastq.gz $samp/${samp}_pass_1.fastq.gz
    ln -fs /groups/nixonlab/telescope_tutorial.git/analysis/$samp/${samp}_pass_2.fastq.gz $samp/${samp}_pass_2.fastq.gz
done

Lets look at what the raw data looks like:

zcat SRR1686362/SRR1686362_pass_1.fastq.gz | head -n4

Lets look at the sequence quality:

module load fastqc
fastqc SRR1686362/SRR1686362_pass_1.fastq.gz
fastqc SRR1686362/SRR1686362_pass_2.fastq.gz

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