What it does

This tool lets you combine the summary statistics, obtained through multiple runs of the Qualimap BamQC tool, of several aligned reads datasets into a single report.

This makes it easy to visualize the degree of similarities between the different inputs and to spot differences between them.

Input

Several Raw Data collections obtained from previous runs of Qualimap BamQC.

Options

Report samples -> Individually / In groups

You may decide to group the input data for reporting, in which case you will need to provide a name for each group that will be used in the plot legends.

Output

The single HTML report generated by this tool contains the following:

Input data and parameters

This section lists the names of the BamQC Raw Data collections that served as input along with the names of the groups (if any) each input got assigned to.

Summary

The summary table contains comparison of selected critical alignment metrics for all samples. The metrics include mean and standard deviation of coverage, mean GC content, mean insert size and mean mapping qualities. If the sample groups are provided, they are also shown for each sample.

PCA plot

The alignment features presented in the Summary section undergo Principal Component Analysis. Afterwards the biplot presenting first and second principal component is constructed. It allows to detect if any samples group together and if there are any outliers among the analyzed samples.

Other plots

Here you will find plots of:

Coverage Across Reference,
Coverage Histogram,
Genome Fraction Coverage,
Duplication Rate Histogram,
Mapped Reads GC Content,
Mapped Reads GC Content Distribution,
Mapped Reads Clipping Profile,
Mapping Quality Across Reference,
Mapping Quality Histogram

and, if applicable,

Insert Size Across Reference,
Insert Size Histogram

Essentially, these are overlays of the plots of the individual inputs (or of the groups they have been assigned to) and that are explained in the help of the Qualimap BamQC tool.