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 5.3).

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Figure 5.3: Select a UMI read mapping.

In the next dialog (figure 5.4), 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.

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Figure 5.4: Specify mRNA and primer tracks.

The tool outputs a primer track with annotated read coverage and a report that recapitulates QC data (figure 5.5). The primer track gives information about each primer, as well as its read coverage, and whether it overlaps with target or housekeeping genes.

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Figure 5.5: QC for RNAscan Panels report.

The QIAseq RNAscan Panels Report

A QC for RNAscan Panels Report contains the following information: