Introduction

Manual assignment of sample types and assays is always possible (except for FastFinder Workflow driven plate setups). In order to automate your plate assignment, sample type nametags are used to recognize your control samples and depending on the cycler you are using, different options are used to recognize your assays. Please find below the correct option for your cycler type.

For full automated plate setup assignment (including the sample names), you can use a .pcrexpertiment file format as explained in this article.

Sample type nametags

Sample type nametags are used to recognize your control samples. You can configure your nametags via Lab configuration - Assays - General - Sample types. These nametags are prefixes of your Sample ID's we read out of the cycler file.

• Click on the “+” sign to add your preferred nametag for automated detection of your control types
• Click on the “x” sign to remove unwanted nametags
• Ask the support team or your project manager to forward you the assay specifications to know the expected result state per control type.

Reporter/target linking

Reporter/target linking is used to assign the correct assay(s). You can manually adjust the reporter and target references in FastFinder under Lab configuration - Assays - PCR tab. In case of multiple cyclers in one assay card, you are prompted to select your cycler first before you can continue.

For melt assays, you need to make sure all target instrument references under one reporter are named the same.

QuantStudio family

For example with the below configuration in the QuantStudio software:

Configure the 'Target instrument reference' and 'Reporter instrument reference' in FastFinder accordingly:

ABI7500

For example with the below configuration in the ABI7500 software:

Configure the 'Target instrument reference' and 'Reporter instrument reference' in FastFinder accordingly:

CFX

For example with the below configuration in the CFX software:

Configure the 'Target instrument reference' and 'Reporter instrument reference' in FastFinder accordingly:

Aria Dx/Mx

For example with the below configuration in the Aria software:

Configure the 'Target instrument reference' and 'Reporter instrument reference' in FastFinder accordingly:

LightCycler 480 Type I & II

For example with the below configuration in the LightCycler software:

Configure the 'Target instrument reference' and 'Reporter instrument reference' in FastFinder accordingly:

Mix name

The automated plate setup for Mic works via Mix name (FastFinder) – Assays (Mic)

Mix names are hardcoded inside the Assay Plugin. You can find the used mix names in FastFinder – Lab configuration – assays – PCR tab. In case of multiple cyclers in one assay card, you are prompted to select your cycler first before you can continue.

Mic

For example with the below configuration in the Assay plugin - 'Mix name':

Configure the Assays in the Mic accordingly:

Mix instrument reference

The automated plate setup for RotorGene works via 'Mix instrument reference' (FastFinder) – Groups name (RotorGene)

Mix instrument references can be manually defined inside the Assay Plugin. You can find the used mix instrument reference names in FastFinder – Lab configuration – assays – PCR tab. In case of multiple cyclers in one assay card, you are prompted to select your cycler first before you can continue.

RotorGene

For example with the below configuration in the RotorGene software:

Configure the Mix instrument reference in FastFinder accordingly:

Manual plate assignment

"?" workaround to assign the correct assay

In case the automated plate setup is not working, but you have defined the correct sample type nametags, select all used wells and use the “?” to assign the correct assay (in the PCR setup tab of an analysis).

Manual plate assignment

In case the automated plate setup is not working, and you have not defined the correct sample type nametags, drag and drop the regular and control tags to assign the correct assay and sample types

Full automated plate assignment

.pcrexperiment files are zip files that combine the analysis file from the cycler with a .pcrsetup file containing the plate information.

• The name of the .pcrsetup file needs to be the same as the analysis file
• Format for the .pcrsetup file (.csv)
  
• Additional information: see FastFinder Analysis PCR setup 2.1_2022MAR08_1_F1.0.pdf

.pcrexperiment files can also be used to upload multiple plates at once automatically via the upload script. Combine the plates in a zip file with .pcrexperiment extension.

Troubleshoot your automatic plate setup

What can I do if I have setup the automated plate setup and the file still appears for manual PCR setup?

• Check if you have setup the reporter/target linking for the correct PCR cycler:
  • Lab configuration – assays – PCR tab – PCR cycler option in the header.
• Check if you don’t have multiple versions of the same assay activated.
  • Activate only the latest plugin version.
• Send your analysis file, assay name and version number to support@velsera.com with a reference to your FastFinder URL for further troubleshooting.

What can I do if I don’t see any assays to assign?

• Check if you have uploaded your Assay Plugin – instrument combination via Lab configuration - assays.
  • Upload a new assay via Lab configuration – Assays – Add new assay. In case you can not find your assay – instrument type combination, forward your request to support@velsera.com. Alternatively click on the add existing assay icon to open Lab configucation - assays ()
  • Check if your Assay Plugin – instrument combination is set to active:
    
• Check if your analysis file contains all targets defined in the plugin to perform the analysis:
  • 
• In case your laboratory has access to FastFinder Studio, clicking on add new assay () in the PCR setup tab will allow you to create your own Assay Plugin compatible with your runfile. Check Analysis - PCR setup for more details on easy AP creation.

What can I do if I see my assay, but cannot assign it to a well?

Contact support@velsera.com for further troubleshooting.

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