Combining reports

At this point, we can summarize all the work done by using the tool MultiQC. MultiQC aggregates outputs from many bioinformatics tools across many samples into a single report by searching a given directory for analysis logs and compiling a HTML report.

First, link our mapping results to the directory QC:

cd QC/
ln -s ../alignments/* .

Then run multiqc on the directory QC to combine all reports:

$RUN multiqc .
[INFO   ]         multiqc : This is MultiQC v1.7 (7d02b24)
[INFO   ]         multiqc : Template    : default
[INFO   ]         multiqc : Searching 'QC/'
Searching 70 files..  [####################################]  100% 
...

and visualize the final report in the browser:

firefox multiqc_report.html