QC for RNAscan Panels

The QC for RNAscan Panels tool can be found in the Toolbox here:

        Toolbox | Biomedical Genomics Analysis (Image biomedical_folder_closed_16_n_p) | QIAseq Tools (Image qiaseq_expert_folder_closed_16_n_p) | QC for RNAscan Panels (Image qc_rna_panels_16_n_p)

Specify a RNA-Seq read mapping as input (figure 5.1).

Image qcfusion1
Figure 5.1: Select a UMI read mapping.

In the next dialog (figure 5.2), specify the mRNA track and the primer track that are saved in the CLC_References folder of the Navigation Area when downloading the QIAseq RNAscan Panels hg38 reference data set. You can also set a maximal distance between a read and a primer start for them to be considered matching. It is set by default to 0, which means that a read will not be considered as starting in the primer unless it maps exactly to the start of the primer.

Image qcfusion2
Figure 5.2: Specify mRNA and primer tracks.

The tool outputs a primer track with annotated read coverage and a report that recapitulates QC data (figure 5.3). The primer track gives information about each primer, as well as its read coverage, and whether it overlaps with target or housekeeping genes.

Image qcfusion3
Figure 5.3: QC for RNAscan Panels report.


The QIAseq RNAscan Panels Report

A QC for RNAscan Panels Report contains the following information:

This report can be used together with the Combine Reports tool (see http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Combine_Reports.html)