3.2 Interpretation of RNAseq processing results using the multiQC report

The nf-core/rnaseq pipeline generates a multiQC report which consolidates all quality control (QC) metrics from the pipeline run.
We will be analyzing the multiQC report from processing the entire dataset - which we have done prior to this course - rather than the one generated in your test run.

The multiQC reports summarizes important QC metrics from RNAseq data processing. This includes for example:

• Tabular overview of general statistics
• QC metrics from FastQC and other software tools, e.g. read quality scores, GC and adaptor content before and after read trimming, % duplication, % read alignmnt, etc
• PCA plot and Euclidean distance heatmap
• Versions of the software tools used (see the end of the report)

Please take a few minutes to inspect the multiQC report. You can use the left panel for navigating the report. We will discuss details and your questions afterwards.

The three control samples are C1, C2 and C3.
The three saccharin treatment samples are sac1, sac2and sac3.