Start a new Design

Publication Number MAN0010907 - Ion AmpliSeq Designer 7.4: Getting Started (5.9 MB PDF download)

If you are using one of the AmpliSeq standard genome references, starting a new design is a relatively simple process. The redesigned website has eliminated some screens to speed the process.

If you are not on the home page, click the “home” icon in the navigation bar to return to the main page.

  1. Enter a Design Name and, optionally, details. The Start a new design page now expands to add additional elements for creating a new panel. New Design Widget
  2. Select your Application type. Choose DNA Gene designs (multi-pool), DNA Hotspot designs (single-pool), RNA Gene Expression designs (single-pool), or RNA Gene Fusion designs (multi-pool). Clicking on the application type filters the compatible genomes below. Note: Custom reference genomes are currently only compatible with DNA designs. RNA Gene designs are only compatible with the human genome.
  3. Select the DNA Type. Choose cfDNA (140 bp), FFPE (175 bp), Standard DNA (275 bp), or Standard DNA (375 bp).
  4. Select a Reference Genome. For custom references, click Custom Reference.
  5. Click Next: Add Targets to proceed.
  6. You have three options for adding targets: Add Gene/Region manually, Add Amplicons by ID, or Upload File.
    • Add a Gene/Region allows a variety of manual options:
      1. Choose type: Gene (CDS only), Gene (CDS +UTR), or Region.
      2. Begin typing the gene symbol or region.
      3. Click Add target after each entry. A green or red text box appears after each to let you know if the target was added successfully.
      4. When finished, click Submit targets.

    • Add Amplicon by ID Allows you to enter amplicon IDs assigned to specific genomic coordinates.
    • Upload File allows you to upload genomic coordinates of several targets at once, via a CSV or BED file (choose from the “Type” dropdown): For guidelines regarding file specifications and restrictions, click the “Input Specifications” link. After browsing and choosing your file, click Upload to proceed.
  7. For any highlighted erroneous target(s), either correct the coordinates inside the table or remove them by checking their checkbox(es) and clicking the Delete button.
  8. (Optional) Click Export targets to download your targets into a CSV file.
  9. To submit your panel, click Submit targets. Five designs can be submitted at a time.
  10. Confirm your submission. Note: If you submit Five designs, you will see this Confirmation pop-up: If you submit three designs, you will see this Alert message:
  11. Once confirmed you will see the following confirmation and also receive an email confirming the design submission.
  12. When the Assay Design results are ready, you will receive an email instructing you to review the results in Ion AmpliSeq Designer. Click the View results provided in the email to be directed to the results page (or navigate to and click the notification or navigate to the completed design using the My Designs tab).

    1. Switch design: Click the drop down to change the design in view.
    2. Edit: Allows you to edit the Design Name and Details only.
    3. Copy Targets: Allows you to copy your design if you want to make modifications to it:
    4. Add to cart and request quote: When this button is green you may click it to add the highlighted design to your cart. Note: If there are not enough amplicons (at least 12) the button is greyed out and the following message appears:
    5. Download results: Design data results are available for download once your assay design is complete. A compressed folder will download containing a number of results files.
    6. Sharing: Allows you to share your designs to another Ion AmpliSeq Designer account holder. Note: Sharing your design also makes your custom reference available for review and downloading by anyone to whom you provide the link to the design.
    7. Export targets: Downloads your targets into a CSV file.
    8. Copy Amplicons: Allows you to copy your amplicons and download an amplicon list or copy your amplicons to another design.
    9. View Cart: Once you add your designs to your cart you may view the cart and request a quote.