How to use the Cloning Validation tool

Visually group your reads into clones and then map them to your reference(s). If you have a naming format for your reads and your reference(s) that meets the requirements below then this process can be automated. Please follow the steps below that are relevant to your workflow.

 

Naming format requirements to automate use of the Cloning Validation tool:

All your reads must have a consistent naming format.

This means they require the same number of parts with the same type of part in the same place for all reads. For example:

reference0-clone1_forwardprimer_A01.ab1

 

All your references must have a consistent naming format.

This means they require the same number of parts with the same type of part in the same place for all references. For example:

experiment1_reference0_location1_A1

 

If grouping into clones, there must be a part of your read name that specifies the clone.

For example, the following would be grouped into two clones: clone1 and clone2.

 

reference0-clone1_forwardprimer_A01.ab1 

reference0-clone1_reverseprimer_B01.ab1

reference0-clone2_forwardprimer_C01.ab1

reference0-clone2_reverseprimer_D01.ab1

 

If you have identical clone names that map to different references, select the part of the name that specifies the reference as well as the clone. For example:

 

reference0-clone1_forwardprimer_A01.ab1 

reference0-clone1_reverseprimer_B01.ab1

reference1-clone1_forwardprimer_C01.ab1

reference1-clone1_reverseprimer_D01.ab1

 

There must be a part of your read name that matches a part in your reference name.

To automatically map your reads to your reference(s), there must be a part of the name of both read and reference that match. For example:

1_reference0-clone1_forwardprimer_A01.ab1

reference0-clone1

 

How to use the Cloning Validation tool:

1. Select your data and open the tool

Select all your reads and reference(s) and click on Cloning Validation in the Cloning menu.

 

2. (Optional) Group your reads into clones

Automatically

Click on the Automatically group by button and select the parts of your reads name(s) that define the clone, then click OK.

 

Manually

Select the reads from your clone, click on the Actions button and select Group Selected. Once you have grouped reads, you can drag additional reads into groups. 

 

3. Map your reads to your reference(s)

Automatically

Click on the Automatically map by button and select the part of your reference name(s) that match the part of a name in your reads/clones, then click OK.

 

Manually

You can drag and drop selected reads/clones from the list of reads to the relevant reference. Alternatively, you can select your reads/clones and click on the Actions button or the [...] button within grouped reads.

 

4. Configure mapping options

When you are satisfied with the optional grouping of reads into clones and mapping to reference(s), click Continue. The default trimming and mapping settings should be appropriate for most circumstances but are configurable in this step. When you are satisfied with these settings, click Continue to perform batch cloning validation.

 

5. Validate your reads/clones

And that’s it! Navigate through your reads/clones to determine validation. We are interested in automating this part validation process, specifically batch filtering based on select criteria and assigning as valid. if this would be useful to you please let us know at support@geneious.com.

 

Tips

Formatting your data for automation

  • To edit the names of your sequences in batch, select the sequences (before using the Cloning Validation tool) then click on the Edit menu from the main menu and select Batch Rename. 
  • If you want to remove parts of a name for automation purposes but want to keep the name for meta data purposes you can add a metadata field and move the data to that field or copy the name to description for safekeeping. Use Batch Rename to copy the contents of the name to another field.

Automating grouping and mapping with multiple naming formats

  • If you have multiple naming formats simply perform the automatic grouping and mapping steps multiple times with the relevant read/reference template.

Using automation as well as manual grouping and mapping

  • In addition to being able to use the automatic grouping and mapping, you can partially automate and partially manually assign your clones and reference mapping.
  • You can manually group reads into clones after they are mapped to their reference but you can only perform this step automatically prior to mapping to their reference.

Adding more reads or reference sequences

  • To add more reads, select + Add more reads, found at the bottom of the reads list
  • To add more references, select + Add another reference, found at the end of the reference list.

Converting reads to references and references to reads

  • Assign reads as reference sequences by selecting the read, clicking on the Actions button and then selecting Convert read to reference.
  • Convert a reference to a read by clicking on the [...] button to the right of the reference name and selecting Convert reference to read.

Resetting grouping and mapping

  • To reset all groupings, select all, click on the Actions button and select Ungroup all.
  • To reset mapping to references click the Reset mappings button.
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