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Resulting in a report that includes our new Mapping quality and Genome coverage sections, that should look like this: http://web.corral.tacc.utexas.edu/iyer/byteclub/multiqc/07_custom_bargraph.mqc_report.html.
Making MultiQC run faster and be less confused
By default, MultiQC scans all files in the analysis directory you specify. This can take quite a while for complex directory hierarchies with many files that will not be used by MultiQC.
Additionally, MultiQC can get confused when the same (or similar) data is found in different files, or in different directories.
To address these issues, it is a good practice to copy everything you want MultiQC to process into a single directory, then either specify just that directory on the multiqc command line (e.g. multiqc for_multiqc), or exclude other directories in the multiqc_config.yaml file.
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Alternatively, you could exclude the bowtie2 directory entirely via a fn_ignore_dirs section list item in multiqc_config.yaml, like this:
| Code Block |
|---|
fn_ignore_dirs:
- bowtie2 |
In either case, the final report should look just as it did for the previous section: http://web.corral.tacc.utexas.edu/iyer/byteclub/multiqc/08_final.mqc_report.html.
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