Checking the quality of the mapping

Qualimap MultisampleBAMQC checks all samples simultaneously

Please note that Qualimap BAMQC makes a report for each sample.

MultisampleBAMQC will make a report for all the samples combined. As input it uses the raw data of the BAMQC reports of the individual samples. When there are groups of samples, set Report samples to In groups. Assign each sample to a group.

The most important feature in the HTML report generated by this tool is the PCA plot. Each sample is a dot on this plot. After assigning samples to groups, the samples in the plots belonging to the group will have the same color. On this plot you do not want to see outliers. If you see an outlier you have to find out why this sample is behaving differently from all the other samples.