Visualizing amplicons

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To view the position of the amplicons for each target, select the UCSC link on the panel details page. This provides a visual display in the UCSC Genome Browser of the submitted target, the amplicons covering it, and the target areas that are not covered.

The target regions submitted to Tapestri Designer are in blue. The areas covered by the inserts are in green. The target regions not covered by the panel (assuming 2x150 bp sequencing) are in red. For more information on missed targets view this article


Use the interface within the UCSC Genome Browser to overlay additional tracks to display the coverage of the SNP databases.


Additional custom tracks can be loaded into the browser using the "Custom Tracks" command in the "My Data" menu. This can be useful to load the Amplicons.bed file found in the designer zip to help visualize where the primers are in relation to targets.  

Custom panels built on UCSC genomes can be visualized, but the .bed files may need to be edited such that the db field matches the UCSC genome name. In the example below, hg19_chrM would need to be changed to hg19.

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