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Microbial samples

cesve edited this page Sep 20, 2018 · 69 revisions

Ordering of sequencing, raw data delivery and in some cases microSALT analysis, of microbial samples.

When submitting an order it will be registered at Clinical Genomics and also create a ticket in Support System. All communication concerning the order should be held through the created ticket. If a ticket concerning the new order already exist, see information in sections below, on how to connect them.

An order can be submitted in two ways: using an Excel based orderform that can be uploaded or by adding samples, one at the time, in our web form at the Orderportal. Both ways are described below.

Using an orderform

Always use the latest version of the orderform, it can be found here.

  • Download the file named Orderform for microbial samples WGS available as an attachment when pressing the link.
  • Fill in information using all fields marked as required in the order form.
  • If needed, use the non-required fields for extended information.

If submitting several samples (typically more than 88) several orderforms can be used, preferably one form for each plate. It's important that the different plates have unique plate names. If not, the orderportal will keep the samples in editing mode to allow you to edit this before the samples can be saved. The box for Well position will be red, indicating that two samples are placed in the same well. See image below.

More guidance concerning how to fill in the order form can be found in the Information tab included in the orderform.

  • When the orderform is completed and saved, go to the Orderportal.

  • Submit your orderform using the Upload orderform field.

  • When submitting an orderform, the fields for Type and Customer will be filled automatically.

  • Add a name for the order and press Save. To connect the order to an existing ticket in Support System, please name the order with # followed by the ticket number, example #123456.

  • All samples present in the order form, will show up below the order section. Here it will be visualized if some fields in the order form is in-correct or missing.

  • To correct the errors, make the changes directly in the Orderportal and press Save the changes.

  • Or, use the Reset order, make changes in the orderform and upload the changed version.

  • If all samples are registered in a correct way, they are visualizes as in image below.

Wanting to add more samples to the same order? Add them one by one by using the button Add sample (se description below Filling out the web form on how to) or upload the next order form.

  • To submit the order, press the Submit order button.
  • A summary of the order will come up, see image below, and needs a confirmation.
  • Check that the summary seem correct, number of samples etc, and confirm it using the Are you sure? button, the order will then be sent to Clinical Genomics.

Filling out the web form

Placing an order without uploading an orderform is made in two steps: Creating an order and Adding samples to the order. Both steps are described in detail below.

Creating an order

  • Give the order a name and select Microbial WGS as Type in the dropdown menu. To connect the order to an existing ticket in Support System, please name the order with # followed by the ticket number, example #123456.
  • Select your customerID from the dropdown menu Customer.
  • It's also possible to add a general comment for the order in the Comment on Ticket field.
  • Press the Save button.

Add samples to the order

  • Press the Add sample button.
  • Fill in the required information, marked with red borders in image below .

  • Comments and additional information (e.g. concentration and volume) connected to the specific sample can be added in remaining fields.
  • When all information concerning the specific sample is registered press the Save button.
  • Keep on adding samples with the Add sample button.
  • When all samples are saved press the Submit order button.
  • A summary of the order will come up, check if the summary seem correct, number of samples etc.
  • When everything seem correct, send the order to Clinical Genomics by using the Are you sure? button.

Troubleshooting

Uploading the order form doesn't work.

  • Please check that the latest version of the orderform is used. Compare to the version found here.
  • Make sure that the options in dropdown menus are used when available.
  • Copying and pasting in the orderform can destroy underlying formats. Download a new orderform here and try to add the information again.
  • If nothing of the above solution works or can be applied please contact Clinical Genomics through Support System.
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