Processing Tracefiles - 96 Well Plate interface

If you are going to produce and process your sequences one plate at a time, the 96 Well Plate interface provides you with your starting point for processing your tracefiles.

To begin, first select 'Process Tracefiles' from the 'Phineus' menu

This will open the import and processing view.

You should then select the button marked 'Select Tracefiles'

This will open a dialog box where you can select your tracefiles.

To do this, first navigate to the directory where they are located, and then select the tracefiles you wish to import.

In order to select multiple files select the first tracefile listed, and then press the select key. Then, scroll the window and select the last tracefile listed, while holding down the select key. You should then see that all the tracefiles are highlighted. Press open to select them for import.

You will then see that the wells corresponding to your tracefiles are unlocked.

Next, you need to select the project which corresponds to the tracefiles that you are going to process.

To do this, open the project combobox and select the appropriate project.

Once you have selected the appropriate project, press OK

The wells will then be updated with the available genes in that project, so you can assign the relvent information to them.

For each well you should then input the relevent details. The upper most combobox contains a list of genes, the middle text field is where you enter the strain/identifying name for the organism and the bottom box is where you specify the read direction of the sample in that well.

You can set the genes or read directions present in collumns or rows en masse, to speed up the assignment of the names on the plate.

To do this, first select either the read direction or the gene you wish to use, this is done by selecting the item from the relvent combobox located in the control bar at the top, as shown for read direction here:

Next, you should select the radiobutton next to the combobox to tell Phineus that you are going to change that value en masse.

Then, you can simply press one of the buttons which act as row or collumn labels, and the system will automatically assign the same value to all of the wells in that row or column.

The same can be done with genes, the gene combobox is located below the read direction combo box. To repeat the above with a gene, first select a gene from the combobox, then confirm the selection by selecting the radiobutton next to the box, and finally apply it to a row or column with the buttons representing row/column labels.

Once this is complete you should enter the strain names/identifiers into the text field for each well.

And you can then import the data into Phineus.

The files will be checked to ensure that they are in a readable format, and then they will be copied to your local hard disk.

This will then present you with a new page

You are now ready to start the automated processing of your tracefiles.

To do so, select

Your computer will then process the tracefiles, updating you on its progress as major components of the pipeline are completed.

Once this is complete, Phineus will take you to the Assembly screen, where you can view and edit your tracefiles.

 

<< Back | Next - how to use the Assembly screen to edit your data >>