Designer output files overview

  • Updated

Tapestri Designer outputs 10 files that are downloaded as a .zip file. This .zip file should be submitted to the Tapestri Pipeline without any changes. 

The 4 files at the top level are used to run Tapestri Pipeline.

  1. [panel-id].amplicons
  2. [panel-id].bed
  3. [panel-id].gatk
  4. systemic-variants.blacklist

The Designer folder in the .zip file contains 6 panel files in human-readable format, which are .bed and .csv files.

  1. [panel-id]-amplicon.bed
  2. [panel-id]-coverage-summary.csv
  3. [panel-id]-design-summary.csv
  4. [panel-id]-insert.bed
  5. [panel-id]-missed.bed
  6. [panel-id]-submitted.bed

Review Tapestri Designer’s coordinate system in this article.

Output files to review

Review these files to review the design.

[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 such as gene, dbSNP, COSMIC, and HGVS as these are resolved to regions by Designer, 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 in between the insert region, they cannot be sequenced. 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.

Files required for Tapestri Pipeline

There is no need for users to review the files at the top level of the .zip file, only the files in the Designer folder.

The .amplicons file has the same content as amplion.bed, and the .gatk and .bed files have the same data as insert.bed. But Tapestri Pipeline requires the files to have only the coordinates, while the files in the Designer folder have the header to view the files in the UCSC genome browser. Thus, we need to include duplicates, and users should only review the files in the Designer folder.

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