Monday, 24 October 2016

How do I submit my index information into Lablink?

When accepting sequencing submissions in the Genomics Core, there may be instances where we have to contact you if there is an error with your submission form. The most common problems relate to index information. We have put together some instructions here that we hope should make things easier and help us to get started on your sequencing as soon as we can.

Please only follow these instructions if:
·        The index sequences you have used are visible in the index sequences tab of the submission form
·        There are fewer than 384 samples within your pool.
If the points above are not true, please see section, unspecified index further on in this blog.

1.      Completing the sample/reagent label field

1a. Navigate to the index sequences tab of the sample submission form.

1b. Search for your index sequences

1c. Copy the index name from column C of the index sequences tab, e.g A001-A005 to the column Sample/Reagent Label, of the submission form tab.

Figure 1-index sequences tab of the sample submission form

Figure2-submission form

      2. Completing the UDF/Index type field

2a. Select the correct UDF/Index type from the drop down menu on the submission form tab.
IMPORTANT –please make sure the Index type field matches column B of the index sequences tab. This ensures that your library goes through our acceptance step. Please see the two following examples. 

Example1- I am submitting a Truseq LT library consisting of 5 samples and used indexes A001-A005.
The sample/reagent label on the submission form should read A001-A005.
The UDF/index type should read Truseq LT.

 Figure 3 - The index type field next to these indexes is Truseq LT so this is what should be entered into the UDF/Index type field.



Figure 4- Submission form

In most cases, the Index type will match to the indexes you have used as expected. However there are now multiple kits available which share the same indexes.
Because of this, there may be some cases where the index sequences you select will have a different Index type to the library you have made. (see example 2 below) This may affect you if you are submitting for Nextera XT or Nextera.

Example 2- I used indexes N701-N501, N702-N501, N703-N501, N704-N501. I prepared the libraries using a Nextera XT library prep kit.

The sample/reagent label on the submission form should read N701-N501, N702-N501, N703-N501, N704-N501. The UDF/index type should read Nextera and not Nextera XT. This is because the UDF/Index type needs to match column B on the index sequences tab.


Figure 5 - The index type field next to these indexes is Nextera so this is what should be entered into the UDF/Index type field

 
3. Unspecified Index

If your pool has index sequences not present in the index sequences tab OR if you have a pool which is made up of more than 384 samples, you will need to submit as unspecified index.
In the submission form:
·        Sample/reagent label should read – unspecified
·        UDF/Index type should read –Unspecified (other)
You should submit your pool as one row on the form. Libraries submitted as unspecified index cannot be demultiplexed by the Genomics Core but we do have a demultiplexing guide on lablink which should give some useful information.

Important-since we have no index sequence information, please write in the comments section of the form the index lengths for Index 1 and Index 2. Without this information your sequencing may be delayed whilst we contact you to check these parameters.
Once you have submitted your libraries, the Genomics Core would like to start working on your sequencing as soon as we can.

If the incorrect index type has been selected, we will need to delete your submission and we would ask you to submit again after making changes to your sample sheet and following the instructions above. Of course whilst this guide should be used to help you, we are always here to discuss this with you in person if you have any questions. Alternatively you can contact us on our helpdesk: genomics-helpdesk@cruk.cam.ac.uk
 



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