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mkdir -p $SCRATCH/byteclub/multiqc/02_bowtie
cd $SCRATCH/byteclub/multiqc/02_bowtie
cp ../01_fastq/multiqc_config.yaml .
rm -rf mqc_report*
multiqc .

If all went well, you should now see a mqc_report.html file that looks like this: http://web.corral.tacc.utexas.edu/iyer/byteclub/multiqc/03_bowtie.mqc_report.html, with new sections for Picard and Samtools reports.

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For the first part of the solution, we'll create a modified version of the metrics files, but not in the alignment directory (after all, here we're using a link to Anna's directory, and we don't want to mess with its contents), but in a new for_multiqc directory.

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