Sequence Data QC - mlbendall/telescope_tutorial GitHub Wiki
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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