Which files do I review to ensure my design is correct?

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Review these output files to ensure your design is correct before using Tapestri Pipeline.

[panel-id]-coverage-summary.csv

Review this file, which is similar to the table displayed in Tapestri Designer. It contains additional information like when a target resolves into more than one region. This file lists the regions that a target is resolved to, and you can review and update some of the targets by providing more specific details, such as adding the transcript ID to the HGVS target or a specific region of interest.

This is especially useful when using targets other than region-based because gene, dpSNP, COSMIC, and HGVS are resolved to regions, and you should ensure these are the ones wanted.

[panel-id]-design-summary.csv

 This file lists the targets covered by each amplicon in catalog panels, and the flag for high GC in predesigned and custom panels. Carefully review this file.

[panel-id]-missed.bed

The user interface shows the coverage value for the targets. In case the coverage is less than 100, it means that regions were missed. These are listed in the missed.bed file. The UCSC link in the panel description provides a visual overview, but to look at the exact coordinates, review this file.

For longer targets like exons, multiple amplicons are designed for a target. In this case, there are gaps between the two inserts for the primer sequences that are missed. In addition, Designer also reports regions that would be missed based on the recommended paired-end sequencing with 150 cycles. Although these regions are inside the insert region, they cannot be sequenced using PE 150 sequencing chemistry. Review these missed regions to know exactly which part of the region is missed and ask for adjustments if the region of interest is missed.

For more information on the other Tapestri Designer output files, refer to this article.

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