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Once you have the report back on your local computer, open it and begin looking at it. Unlike the FastQC report, the multiqc report comes with detailed help information for each section you can access with the different ?help icons on the right as well as a video at the top of the page. If anything is not clear, and you'd like help clearing it up, let me know.

Optional Exercise

1. Using information in the MultiQC report, modify the bash loop used to create the fastqc_commands file above to create a cutadapt_commands file that could modify all 544 files at once.
2. Move over to the trimmomatic tutorial and come back to trim all adapter sequences from all files and rerun fastqc/multiqc to see what a difference trimming makes on overall quality.

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