The Run PCR tool takes in a plate map and input plate(s) (or inventory lists) of primary templates and primers. Together these specify how the materials need to be combined to make assembly pieces necessary for a j5 assembly reaction. The tool outputs a worklist, a reaction map, and a destination PCR plate where the PCR reactions will take place.

Input: Plate Map, Input Plates, PCR Inventory List

Output: Worklist, Reaction Map, and PCR Plate


  • (required) The plate map(s) must already exist in data (Data > Plate Map Groups)

  • If the PCR plate map does not exist yet, go to Tools > PCR Planning and Inventory Check to create one. This will require a j5 Report with PCR reactions

  • Choose One or Both of the following:

  • Input Plate(s) of Primary Templates and Primers (if one doesn't exist, go to Inventory > Plates and upload a plate CSV file)

  • A PCR Inventory List of Primary Templates and Primers. This can be output by the Inventory Check step of the PCR Planning and Inventory Check tool.

You can find the Run PCR tool under Tools > Tool Library. Click ‘Launch Tool’ to start using the tool.

The tool will walk you through several steps. You need to complete each step before proceeding to the next. After completing a step, the completed step mark (circle) will turn green with a checkmark. You can always use the ‘previous’ button to go back to previous steps. This tool consists of three steps: Select PCR Source Materials, PCR Configuration, and Review PCR Worklist.

1. Select PCR Plate Map: Begin by selecting your PCR Plate Map.

This will dictate the destination wells for your PCR reactions.

Next select your input PCR samples by choosing either Input Plates, PCR Inventory Lists, or both.

Here is what a preview of a selected Input Plate looks like:

Alternatively, we could also have chosen our samples via the Select PCR Inventory Lists section:

The table at the bottom validates whether all the necessary PCR samples have been selected:

2. PCR Configuration: Specify transfer volumes from the selected input plates to the destination plate.

Don't forget to give the Output Plate a unique name and specify which type of plate you'll be using.

3. Review PCR Worklist: you'll need to name the output Worklist and Reaction Map:

Make sure to look over the worklist preview to verify that the transfers are correct.

If you see an error such as:

This is warning you that your worklist will fail when you try to run it because the input plate does not contain enough volume for the transfers.

If you don't see any errors, give the reaction map a memorable name, and hit "Generate Worklist" to complete the tool.

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