DesignStudio FAQs

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  • AmpliSeq for Illumina On-Demand – IGV Viewer

  • The “observed coverage” track indicates the number of observed reads for each amplicon of each targeted gene during validation experiments on a NextSeq. Use this track as general guidance for the likely performance when running an experiment. While values can vary among assays, the general coverage trend should remain consistent.

    Gaps occur where there are no amplicons to provide coverage for the intended target. We have made every effort to minimize the occurrence of these regions in our On-Demand designs.

    The Y-axis represents the observed coverage normalized by the mean amplicon coverage for the gene.

    No. The IGV viewer can only focus on your gene of interest. In the Grid View, select a gene, and the IGV viewer updates automatically to center on that gene.

    All amplicons in the design contain reads that are visualized in the “observed coverage” track. If the number of reads covering an amplicon is relatively small in comparison to neighboring amplicons, the “observed coverage” track appears empty. However, if you change the scale to a lower value, you will then be able to visualize the lower number of reads. If the observed coverage track is not present, the designer notifies you why that track is not available.

  • Spike-in Panels

  • Custom DNA Panel spike-in to AmpliSeq for Illumina on Demand is a 2-pool panel that allows you to add CDS-only genes that are not available in the AmpliSeq for Illumina On-Demand catalog to your design

    Because there is a limited number of genes available in the AmpliSeq for Illumina On-Demand catalog, a Spike-in panel enables you to sequence all intended targets in a single target amplification reaction.

    Yes, the limitations of Spike-in Panels involve the number of genes that can be included. The maximum size of a Spike-in Panel is 123 amplicons per pool, for a total of 246 amplicons. From a performance standpoint, since Spike-in Panels are manufactured as made-to-order panels and are not wet-lab tested like On-Demand Panels.

    Spike-in Panels follow our made-to-order process and are synthesized de novo at every order. The number of reactions is typically large (750–3,000 reactions). On the other hand, On-Demand Panels have been optimized, premanufactured, tested, and are available in small reaction number batches. On-Demand Panels also contain data that can be visualized in our integrated IGV viewer available in the Grid view.