When you click Create Panel from the Tapestri Designer home page, it displays a page where you specify the genome and enter the target information.

Tapestri Designer supports the entire genome for hg19 (GRCh37), not just the CDS regions of the genome. Users can submit non-CDS regions in any supported target format, except by definition gene, and Designer will resolve it to the corresponding regions and design for it.

The same is true for the mm10 (GRCm38) genome, although Designer only supports the region target type.

If a panel includes any targets in non-CDS regions, however, the processing time will increase because the amplicons must be designed from scratch instead of using cached amplicons.

Step 1: Select the genome

Tapestri Designer supports human genome hg19 (GRCh37) and mouse genome mm10 (GRCm38).

Step 2: Enter the targets

Enter the targets for the custom panel by uploading a .csv file or pasting or typing in the information.

Important: The .csv must use "," as the separator. The EU separator ";" will not work.

To upload a file, drag and drop it into the Upload box or click the Browse File button to locate the file. If the .csv file has a header row, click the File has header checkbox to ignore that information. The file should have three columns: target type, target ID, and target name (optional).

To paste or enter the targets, click the Paste button. Then, paste or manually enter the target information. The format is: target type, target ID, target name (optional). 

Example Tapestri Designer input:

gene, TP53, p52_mutation

region, Chr10:106721610-106721610, variant ABC

dbSNP, rs4880, SOD2 mutation

COSMIC, COSM1041, my variant

hgvs, PIK3CA:C.1633G>A, PIK3CA

Note: The spaces after the commas are optional.

For more information about target types, refer to Target types.

After entering the targets, click the Submit button.

Step 3: Name the panel

Name the panel and provide a description. The maximum length for the name is 100 characters, and the description is 250 characters. Both can contain spaces, numbers, and symbols.

Click the Continue button or the red x to delete the panel.

Step 4: Validate the targets

After entering the target information, the targets must be preprocessed to resolve them to chromosomal regions. hg19 (GRCh37) and mm10 (GRCm38) genome builds are supported.

Important: All coordinates must be entered for one of these genome assemblies in one-based format.

Click the Refresh button to see the latest results or the red x to delete the panel.

A status line shows the number of targets successfully added along with the number of targets with errors, if any.

Errors

If there are errors, two buttons appear:

Show Errors: Click this button to show only the targets with errors.

Remove Errors: Click this button to delete all targets with errors.

To edit targets, such as the type, name, or ID, click the edit icon in the Actions column to the right of the page.

To delete targets, click the red trashcan icon in the Actions column to the right of the page.

Possible errors:

Invalid ID: The format of the ID is invalid. Change the ID to match the required format.

Duplicate Target: Duplicate targets are not allowed. Delete the target.

Invalid Region Target: Region targets are validated to check the chromosome length constraint. Regions with either start or stop values greater than the chromosome length are marked invalid.

Incorrect Target ID Format: If the target ID contains an additional space, it is marked invalid. For example, Chr13: 28674559-28674790 is invalid.

Incorrect Target ID or Name: Target IDs and names do not support commas. If added, they are removed from the targets before creating the panel.

Masked Regions: If the target has many masked regions (Ns in reference fasta for the target), the panel will fail. Avoid adding region targets with these.

Step 5: Add, edit, or delete targets

Click the edit icon next to the panel name in the left panel or description under the Back button to edit that information.

X: Deletes the custom panel.

Save for Later: Saves the panel for later editing. It has a status of Draft.

Continue: Tapestri Designer compares the custom panel to all the catalog panels to see if there is any overlap. 

+ Add Target: Clicking this button adds additional targets. In the dialog, select a target type and enter a target ID and optional target name. Repeat this process for any additional targets you want to add.

Search: Type in either a type, name, or ID to display a list of only those targets.

Click the checkbox to the left of each target to enable the bulk actions menu.

To edit or delete targets, click the icons in the Actions column.

Sort the targets by any column, except Actions, in ascending or descending order by clicking the header name.

Step 6: Overlap resolution

If the targets in the custom panel are similar to any of the catalog panels, a page displays listing the identified panels.

Clicking the checkbox to the left of the catalog panel name displays a separate table listing each of the custom panel’s targets and the overlap with the catalog panel. Information for up to three catalog panels can be displayed in the table at one time.

If a catalog panel meets your needs, save time and effort by using that panel. Click the catalog panel name to display the panel details page where you can request a quote.

Submit: If no panel overlapped with your custom panel or the coverage did not meet your needs, submit your panel. 

After submitting the panel for processing, no further editing is possible.

Step 7: Design

Once you submit your custom panel, it will display in the dashboard on the Tapestri Designer home page as In Progress. You will receive an email confirming that you submitted a panel for processing.

During the processing, amplicons are generated to cover the targets, and the coverage percentage is calculated.

Note: When generating amplicons for a custom panel copied from a catalog panel, it may not include the same amplicons since not all are available in the custom amplicon pool.

When the processing is complete, you will receive notification that the results are ready via an email, which includes the panel and runtime details. The status in the dashboard will change to Ready.

Download the files created by Designer during processing to view the details or use as input into Tapestri Pipeline.

If the panel details page is still open when you receive the email, click the Refresh button to update the information.

Step 8: Review results

The details of the panel display, along with any warnings. For a detailed explanation, refer to the panel details page.