Tapestri Designer User Guide

  • Updated

Mission Bio’s Tapestri Designer is a web-based primer design tool that allows you to explore predesigned DNA panels or create custom ones that can be used in a multi-omics solution for simultaneous detection of single-nucleotide variants (SNVs), copy number variations (CNVs), and proteins from the same cell.

Key Features

  • Order inventoried or pre-designed catalog panels.
  • Create custom panels with targets and the genome of your choice.
  • Visualize amplicons for the panels using the UCSC link to see a visual display of the target coverage. This only applies to hg19 and mm10 catalog genomes.

Table of Contents

  1. Log In
  2. Settings Menu
  3. Create a Custom Panel
  4. Custom Panels Details
  5. Tapestri Designer Dashboard
  6. Catalog Panels
  7. Catalog Panel Details
  8. Output Files

Log In

To get the most out of Tapestri Designer, log into your Mission Bio account on Tapestri Portal. The functionality depends on several factors.

If you are not logged in, a new user, or have no custom designs:

When not logged into your Mission Bio account, you can only view the list of catalog panels and their target details. For any other action, such as downloading or copying a panel or creating custom panels, you must log into your account.

As a new user or someone without custom designs, Tapestri Designer’s home page displays options to browse our catalog panels and create a custom panel. 

Logged in with at least one custom panel:

When logged in and you have access to at least one custom panel, a dashboard displays at the bottom of the home page listing the panels.

Settings Menu

Click on your name in the top-right corner. A drop-down menu will appear.

SettingsMenu.png

Home
Click the Home menu item to navigate to the Designer home page.

Support
Click the Support menu item to go to the Support Center.

Logout
Click the Logout menu item, to log out of Tapestri Pipeline.

Create a Custom Panel

On the home screen, click Create Panel.

CreatePanelButton.png

The custom panel creation screen will appear.

Step0.png

Name the Panel

  • Panel Name: Provide a name for the panel. It can be up to 100 characters, consisting of letters, numbers, special characters, and spaces.
  • Description: Enter an optional description for the panel. It can be up to 250 characters, consisting of letters, numbers, special characters, and spaces.
  • Click Next.

Step 01 – Select Parameters

  • Assay Type: Preset. Currently, Tapestri Designer supports only the DNA assay.
  • Amplicon Length Range: The amplicon length range is preset to 175 – 275 bp.
  • Genome: Select the genome of choice from the drop-down menu. Tapestri Designer provides catalog human genome hg19 (GRCh37) and mouse genome mm10 (GRCm38). Additionally, you may upload your own by following the steps provided here. Any previously uploaded genomes will be listed in the menu.
  • Click Next.

Step 02 – Upload Targets

Enter the targets for the custom panel by uploading a .csv. Alternatively, paste or type the target information. 

Important: The .csv must use a comma (“,”) as the separator. The EU semicolon separator (“;”) will not work. Download sample file template.

  • Upload File: To upload a file, drag and drop it into the box. Or click Choose File to locate the file. If the .csv file has a header row, click the File has a header (skips the first line) checkbox to ignore that information. The file should have two columns with an optional third – target type, target ID, and target name (optional).
    Step02-UploadFile.png
  • Add Targets: Click Add Targets to paste or manually enter the targets. If the pasted targets have a header row, click the File has a header (skips the first line) checkbox to ignore that information. 
    Step02-AddTargets.png

Target Formats

Targets must be in this format: target type, target ID, and 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

Notes 

  • The spaces after the commas are optional. 
  • Only the hg19 catalog genome supports all targets. Please use ‘region’ targets for all other genomes.
  • Gene names are case-sensitive.
  • Duplicate targets are not allowed.

For more information about target types and a sample .csv file, refer to Target types.

  • After uploading the targets, click Next.

Step 03 – Review Targets

After entering the target information, the targets will be preprocessed to resolve them to chromosomal regions. The status of your panel will be Preprocessing.

  • Click the Refresh icon to see the latest results.

Once the targets have been preprocessed, the panel status will change to Draft.

If the panel contains any targets with errors, those targets need to be edited or removed to proceed further.

EditTarget.png

  • To edit a target, such as the type, name, or ID, click the edit icon next to the target. Click the green checkmark to accept the change, or the red “x” to revert the change.
  • To delete a target, click the trashcan icon, and click Delete Target.

Possible Errors

  • Invalid ID: The format of the ID is invalid. Change the ID to match the required format.
  • Duplicate Target: Neither duplicate target ID nor Names are allowed. Edit or 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 cannot contain commas. When 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.
    SearchTarget.png
  • Add Target: To add more targets, click Add Target.
    In the pop-up screen, select the Target Type, enter Target ID and an optional Target Name. Repeat this process for any additional targets you want to add.
    AddTargetModal.png
  • Search: Type in either a type, name, or ID to display a list of only those targets.
  • Bulk Actions: Click the checkbox to the left of each target to enable the bulk actions menu.
  • Sort: Sort the targets by any column in ascending or descending order by clicking the header name.

Step 04 – Submit Panel

Panels created using the hg19 (GRCh37) catalog reference may have overlapping targets with Mission Bio’s catalog panels. If your panel contains overlapping targets, you can explore the catalog panels in Step 04. 

Step04.png

  • To compare the catalog panels, select the checkbox to the left of each catalog panel. A Compare Target Overlap table listing each of the custom panel’s targets and the overlap with the catalog panel will appear. Information for up to three catalog panels can be displayed in the table at one time.
    CompareTargetOverlap.png
  • If a catalog panel meets your needs, save time by using that panel. Click Explore to the right of 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, click Submit to submit your panel.

In Progress

Once you submit your custom panel, the Panels Details page will display with a status of In Progress. It will also 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. When the design is complete, you will receive another email.

Note: After submitting the panel for processing, no further editing is possible. To include more targets, click on the three vertical dots in the Custom Panels dashboard next to the Panel name. Select Copy Targets. This will create a new custom panel where you can add more targets. Only the targets are copied, not the amplicons.

ContextMenu.png

Ready

When the processing is complete, you will receive notification that the results are ready via an email, which includes the panel 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.

Custom Panels Details

Click on a custom panel name from the Custom Panels Dashboard to open the Panel Details page. The details are presented in two sections. The top section displays the panel details, and the bottom section displays the target details. 

CustomPanelDetails.png

Top section – Panel details

The top section of the panel details page presents the panel details.

  • Panel Name: The name of the panel provided during panel creation.
  • Description: The description of the panel provided during panel creation.
  • Coverage: The percentage of the target base pairs covered by the insert regions. It is the in-silico R1R2 coverage value of the panel calculated using 150 bp as the read length for paired-end sequencing.
  • # Targets: The number of targets in the panel. Details about these targets display in the bottom table of the page. Each target is a separate line in the list.
  • Target Size: The target size is the total number of DNA base pairs covered by all the targets in the panel.
  • Panel Size: The panel size is the total number of DNA base pairs covered by all the inserts in the panel.
  • Amplicon Length Range: The amplicon length range is preset to 175 - 275 bp.
  • # Amplicons: The sum of all the amplicons generated to create the best possible coverage of all the targets.
  • Validated: No for custom panels because these are not experimentally validated.
  • Assay Type: Currently, Tapestri Designer only supports DNA.
  • Genome: Tapestri Designer provides human genome hg19 (GRCh37) and mouse genome mm10 (GRCm38). Additionally, you may upload your own by following the steps in this document.
  • Warning: Some panels contain amplicons that are positioned in high GC regions. In this case, a warning displays at the top of the page, and the impacted targets display a yellow triangle to the left of the target ID.
  • More Actions: Click More Actions to access additional features:
    MoreActions-Share.png
    • Download Results: Click the Download Results button to download a .zip file that contains the output files exported from Tapestri Designer.
      For more information on these files, refer to this section.
    • Copy Targets: Click the Copy Targets button to create a new custom panel based on the current panel. Only the targets are copied, not the amplicons.
      For more information about creating custom panels, refer to Create a custom panel.
    • Share: Click the Share button to share the custom panel with other users. The Share screen will appear.
      ShareModal.png
      • In the Email field, add the email IDs of other users who have an account on Tapestri Portal, separated by either a comma (,) or semicolon (;). 
      • Add personal Notes up to 10,000 characters, and click Save.
        This sends an email to the recipients’ email IDs. Those users can then access the shared panel after logging into Mission Bio Portal. Once you share a panel, you can never delete it. The people you share it with can delete it, however.
      Note: Panels can only be shared with existing users who have an account on Mission Bio Tapestri Portal and have opened Tapestri Designer. Once those two conditions are met, panels can be shared with them.
    • Delete: Click the Delete button to permanently delete the custom panel. If a panel has been ordered or shared, it cannot be deleted.
  • Request Quote: Click Request Quote to send a message to Mission Bio. Someone from our team will contact you soon. Sales are completed offline.
    RQ.png

Bottom Section – Target Details

The bottom section of the Panel Details page shows the details of the targets.

  • Search: Type in a target name or ID to quickly locate that target.
  • Each target is listed with the following information:
    • Type
      • Gene: Official HGNC gene name. Applies only to catalog genome hg19 (GRCh37).
      • Region: Chromosome coordinates from the selected genome assembly.
      • dbSNP: dbSNP ID. Applies to only catalog genome hg19 (GRCh37).
      • COSMIC: COSMIC database ID (v84). Applies only to catalog genome hg19 (GRCh37).
      • HGVS: HGVS nomenclature supported by VarSome. Applies only to catalog genome hg19 (GRCh37).
    • Target ID: The ID is based on the target type.
    • Target Name: This optional field is a text identifier for the target to make it understandable to the user. Each name should be a unique identifier within a panel.
    • # Amplicons: The number of amplicons for the target.
    • % Coverage: The insert coverage of the target. 
    • UCSC Link: Clicking the UCSC link displays the target in the UCSC Genome Browser. For more information, refer to Visualizing amplicons. Applies only to catalog genome hg19 (GRCh37) and mm10 (GRCm38).
  • Sort: Sort the targets by any column, except the UCSC Link, in ascending or descending order by clicking the header name.

Tapestri Designer Dashboard

The dashboard has two tabs. The Custom Panels tab lists each custom panel. The Custom Genomes tab lists each custom genome uploaded to your account. 

Custom Panels

The dashboard lists the following information for each custom panel.

CustomPanels.png

  • Panel Name: The panel name has a maximum length of 100 characters and can contain spaces, numbers, and symbols. Clicking on a panel name that is in Draft mode opens the panel creation workflow. Clicking on a panel name that is in In Progress, Ready, or Failed opens the Panel Details page, which displays all the information about it.
  • ID: The panel ID is a unique number and automatically generated. This number cannot be changed.
  • Genome: The genome name used to create the custom panel. Tapestri Designer provides catalog human genome hg19 (GRCh37) and mouse genome mm10 (GRCm38). Additionally, you may upload your own by following these steps. All coordinates in the panel should belong to the selected genome assembly.
  • # Targets: The total number of targets in the panel.
  • # Amplicons: The number of amplicons is displayed for panels that have a status of Ready. It is calculated when you submit the panel for processing.
  • % Coverage: The coverage percentage is displayed for panels with a status of Ready. It is calculated when you submit the panel for processing. It is the percentage of the target base pairs covered by the insert regions. It is the in-silico R1R2 coverage value of the panel calculated using 150 bp as the read length for paired-end sequencing.
  • Last Updated: The date of the last edit to the panel.
  • Created By: The email address of the owner who created the panel.
  • Status: The current status of the panel. 
    • Preprocessing: The targets in the panel are being resolved to chromosomal regions.
    • Draft: The panel has not been submitted for processing. The panel can be edited to add, edit, and delete targets.
    • In Progress: The panel was submitted for processing, and Mission Bio is working on generating the amplicons and coverage percentage. The panel can no longer be edited. You will receive an email when processing is complete.
    • Ready: The process is complete. The amplicons were generated, and the coverage calculated. The panel can be viewed, copied, and shared but not edited. You can also Download Results. These options are available by clicking on the three vertical dots next to the Panel Name.
    • Failed: No amplicons were generated, so the panel is not valid.
  • Search: To search for specific panels, type the criteria into the search box. You can search for:
    • Panel Name
    • ID
    • Genome
    • # Targets
    • # Amplicons
    • % Coverage
    • Status
  • Refresh Icon: Click the Refresh icon to update the status of custom panels.
    RefreshIcon.png
  • Sort: Sort the panels by any of the columns in ascending or descending order by clicking the header name.

Custom Genomes

To access information on the catalog genomes and custom genomes you uploaded, click the Custom Genomes tab.

CustomGenomes.png

The dashboard lists the following information for each genome:

  • File Name: The file name of the genome .fasta file provided at the time of upload.
  • BED File Name: The polymorphism .bed file name provided at the time of upload.
  • Genome Name: The genome name provided at the time of upload.
  • Status: The status of the file upload. 
  • Uploaded Date: The date of the file upload. 
  • Genome Size: The size of the genome post processing. 
  • Uploaded By: The email account used to upload the file.
  • Common Name: The common name provided at the time of upload.
  • Scientific Name: The scientific name provided at the time of upload.
  • Assembly Version: The assembly version provided at the time of upload.
  • # Contigs: The total number of contigs provided at the time of upload.
  • Search: To search for specific files, type the criteria into the search box. You can search for:
    • File Name
    • BED File Name
    • Genome Name
    • Status
    • Uploaded By
    • Common Name
    • Scientific Name
    • Assembly Version
    • Contigs
  • Refresh Icon: Click the Refresh icon to update the status of custom genome uploads.
  • Sort: Sort the genomes by any of the columns in ascending or descending order by clicking the header name.

Upload Genome

To upload a custom reference file, click the Upload Genome button.

The Custom Genomes screen will appear. Fill in the details in the input fields. 

UploadCustomGenome.png

  1. Genome Name: Must be between 3 and 50 characters, consisting of letters, numbers, and supported special characters: hyphen (-) and underscore (_). 
  2. Common Name: The common name of the organism the sequences belong to. Must be between 3 and 50 characters, consisting of letters and numbers.
  3. Scientific Name: The scientific name of the organism the sequences belong to. Must be between 3 and 100 characters, consisting of letters and numbers.
  4. Assembly Version: The genome version of the custom reference file must be between 1 and 20 characters, consisting of letters and numbers.
  5. # Contigs: Total number of contigs in the file.
  6. Genome FASTA file: Select the custom reference .fa file. For file specifications, please refer to this document.
  7. Polymorphism loci on primers BED file (optional): Select a polymorphism .bed file containing the regions of high polymorphism. For file specifications, please refer to this document.

To save your custom reference file, click Submit. This starts the uploading process. The file will be added to the table of Custom Genomes with a status of Processing. The upload time varies based on the reference file size. Once the file completes uploading, the status of the custom reference file will change to Completed. 

This reference file will now be available for use when creating custom panels in Step 01 - Select Parameters. The drop-down menu for Genome selection will list the file with the Genome name provided.

Note: Once the files have been uploaded, no changes can be made. If you need to make changes, upload the edited files using the Upload Genome button.

Catalog Panels

Clicking the View Panels button from the Tapestri Designer home page takes you to the Catalog Panels page where you can explore the current catalog panel designs.

CatalogPanelsDashboard.png

The pre-selected tab lists the DNA catalog panels. 

The top four panels are experimentally verified and Ready-to-Ship. These are followed by the predesigned targeted panels that are Built-to-Order. These panels have not been verified in a lab. 

Click the Protein tab to access catalog protein panels.

Catalog Panels Dashboard

The dashboard lists the following information for each catalog panel:

  • Panel Name: The name of the panel. 
  • Panel Type: The type of the panel, whether the panel is Ready-to-Ship or Built-to-Order.
  • Genome: The genome of the panel.
  • # Targets (DNA only): The number of targets in the panel.
  • # Amplicons (DNA only): The number of amplicons covering the targets.
  • % Coverage (DNA only): This number describes how well the amplicons cover the targets.
  • # Antibodies (Protein only): The number of antibodies in the protein catalog panel.
  • Validated: True for panels that have been validated in a lab. False for panels that have not been validated.
  • Last Updated: The date of the last edit to the panel.

Navigation

  • Search: To search for specific panels, type the criteria into the search box. You can search for:
    • Panel Name
    • Panel Type 
    • Genome
    • # Targets
    • # Amplicons
    • % Coverage
    • Validated
  • Details: Click the panel name to open the catalog panel details page and view additional information.
  • Sort: Sort the panels by any of the columns in ascending or descending order by clicking the header name.
  • Download Results: Click on the three vertical dots next to the Panel name to download the results.
  • Copy Targets (DNA only): Click on the three vertical dots next to the Panel name to copy the targets and start designing a new custom panel. Only the targets are copied, not the amplicons.

Catalog Panel Details

Click on a catalog panel to open the Panel Details page. The details are presented in two sections. The top section displays the panel details, and the bottom section displays the target details. 

CatalogPanelDetails.png

Top Section – Panel Details

The top section of the panel details page displays the panel level information:

  • Panel Name: The name of the panel.
  • Description: A description of the panel.
  • Coverage (DNA only): The percentage of the target base pairs covered by the insert regions. It is the in-silico R1R2 coverage value of the panel calculated using 150 bp as the read length for paired-end sequencing.
  • # Targets (DNA only): The number of targets in the panel. Details about these targets display on the bottom of the page. Each target is a separate line in the list.
  • Target Size (DNA only): The target size is the total number of DNA base pairs covered by all the targets in the panel.
  • Panel Size (DNA only): The panel size is the total number of DNA base pairs covered by all the inserts in the panel.
  • Amplicon Length Range (DNA only): The amplicon length range is preset to 175 – 275 bp.
  • # Amplicons (DNA only): The sum of all the amplicons generated to create the best possible coverage of all the targets.
  • # Antibodies (Protein only): The number of antibodies in the protein catalog panel.
  • Validated: True for panels that have been validated in a lab. False for panels that have not been experimentally validated.
  • Assay Type: Assay type DNA or Protein.
  • Genome: Tapestri Designer provides catalog human genome hg19 (GRCh37) and mouse genome mm10 (GRCm38). 
  • Warning (DNA only): Some panels contain amplicons that are positioned in high GC regions. In this case, a warning displays at the top of the page, and the impacted targets display a yellow triangle to the left of the target ID.
  • More Actions: Click More Actions to access the following:
    MoreActions-Catalog.png
    • Download Results: Click the Download Results button to download a .zip file that contains the output files exported from Tapestri Designer.
    • Download Datasheet (DNA only): Click the Download Datasheet button to download a .pdf file that contains detailed information about the panel, including the panel specifications and targets. This is only available for the following catalog panels – Tumor Hotspot, Myeloid, Chronic Lymphocytic Leukemia, Acute Myeloid Leukemia, Chronic Myeloid Leukemia, Diffuse Large B Cell Lymphoma, T-Cell Lymphoma, Acute Lymphoblastic Leukemia, Myelodysplastic Syndromes, Myeloproliferative Neoplasms, Classic Hodgkin's Lymphoma, Multiple Myeloma, Mantle Cell Lymphoma, and Follicular Lymphoma.
      For more information on these files, refer to this section.
    • Copy Targets (DNA only): Click the Copy Targets button to create a new custom panel based on the current panel. Only the targets are copied, not the amplicons.
      For more information about creating custom panels, refer to Create a custom panel.
  • Request Quote: Click Request Quote to send a message to Mission Bio. Someone from our team will contact you soon. Sales are completed offline.
    RQ.png

Bottom Section – Target Details DNA

The bottom section of the Panel Details page shows the details of the targets.

  • Search: Type in a target name or ID to quickly locate that target.
  • Sort: Sort the targets by any of the columns, except UCSC Link, in ascending or descending order by clicking the header name.

Each target is listed with the following information:

  • Type: The options are:
    • Gene: Official HGNC gene name
    • Region: Chromosome coordinates from the hg19 genome assembly
    • dbSNP: dbSNP ID
    • COSMIC: COSMIC database ID (v84)
    • HGVS: HGVS nomenclature supported by VarSome
  • Target ID: The ID is based on the target type.
  • Target Name: This optional field is a text identifier for the target to make it understandable to the user. Each name should be a unique identifier within a panel.
  • # Amplicons: The number of amplicons for the target.
  • % Coverage: The percentage of the target base pairs covered by the insert region. It is the in-silico R1R2 coverage value calculated using 150 bp as the read length for paired-end sequencing.
  • UCSC Link: Clicking the UCSC link displays the target in the UCSC Genome Browser. For more information, refer to Visualizing amplicons.

Bottom Section – Target Details Protein

The bottom section of the Panel Details page shows the details of the targets.

  • Search: Type in a protein name, clone name, clone description, or barcode sequence to quickly locate the protein.
  • Sort: Sort the targets by any of the columns in ascending or descending order by clicking the header name.

Each target is listed with the following information:

  • Protein Name: Antibody name.
  • Clone Name: Clone name.
  • Clone Description: Short description for the protein antibodies.
  • Barcode Sequence: 15 bp oligo sequence to identify the antibodies.

Output Files

Tapestri Designer generates 10 files that are downloaded as a .zip file for custom DNA panel files. 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
    This file contains the list of amplicons designed for the submitted targets. For more information, see this file.
  2. [panel-id].bed
    This file contains genomic coordinates for the insert regions of interest. For more information, see this file.
  3. [panel-id].gatk
    This file contains genomic coordinates for the targets that get used in downstream processing in Tapestri Pipeline. For more information, see this file.
  4. systemic-variants.blacklist
    The systemic-variants.blacklist file lists the genomic regions for suspected false-positive variants. The blacklisted variant’s coordinates are used to remove such variants from the final output files.
    The Designer folder in the .zip file contains 6 panel files in human-readable format, which are .bed and .csv files.
  5. [panel-id]-amplicon.bed
    This file lists the coordinates for the amplicons that cover the given input targets. For more information, see this file.
  6. [panel-id]-coverage-summary.csv
    This file contains the coverage information for the given input targets. For more information, see this file.
  7. [panel-id]-design-summary.csv
    This file contains information about the input targets and the corresponding amplicons. For more information, see this file.
  8. [panel-id]-insert.bed
    This file contains the genomic targets for the given input targets. For more information, see this file.
  9. [panel-id]-missed.bed
    This file lists the genomic coordinates for the targets that are not covered or are missed by the amplicons. For more information, see this file.
  10. [panel-id]-submitted.bed
    This file contains information on the user-defined targets that are converted to coordinates. For more information, see this file.
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