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Consider how you might use fastq_quality_filter and fastq_quality_trimmer to limit your data based on quality scores.
Optional Exercise: Improve the quality of R2 the same way you did for R1.
Unfortunately we don't have time during the class to do this, but as a potential exercise in your free time, you could improve R2 the same way you did R1 and use the improved fastq files in the subsequent read mapping and variant calling tutorials to see the difference it can make.