Wetlab Manager role
The Wetlab Manager is the responsible for starting the run in NextSeq, based on the inputs given by the Investigator.
With that information the Wetlab Manager will start the process on iSkyLIMS by starting the run creation, clicking Run Preparation--> Create new NextSeq Run from the top menu.
The NextSeq run creation process has 3 separated steps:
- First. The form to get the "sampleSheet.csv" file provided by the investigator.
- Second. The form to define/confirm the run name and library information.
iSkyLIMS collects this information (if available) from the "sampleSheet.csv" uploaded in the previous step, and show them in the text fields.
This information can be modified if the information in sampleSheet.csv file was missing or incorrect
Run Name:
Is the run name where it will be reference later.
Be aware that for iSkyLIMS workflow to work properly, Run Name MUST match EXACTLY the Run Name configured in "BaseSpace". For instance run name "Next_Seq_CNM_111" and "NextSeq_CNM_111".
A mismatch like this one, makes that when NextSeq sequencer finish its process and create the output files it was no possible to match them and the run remains in Recorded state until the mismatch was solved.
Index Library Name:
This field MUST be set with the same name as it is in BaseSpace, with concordant indexes and name indexes in the sample sheet.
Note that most of the time, libraries in IEM and BaseSpace are compatible, but, if for some reason is not your case please contact your Administrator to provide you a library configuration file for adding a custom one to your BaseSpace account.
Project information:
On this part of the form library information and user responsible for the project is showed. This block of information will be repeated for each of the different projects defined on the uploaded sampleSheet.csv
- User name. A valid userid has to be provided on this field. Submit button will be disable until a valid userid was enter. You can add a new user using the django admin utilities to create a new user. Then reload the page again to fetch all defined user.
Special issues for NextSeq and BaseSpace:
Sample sheet file MUST contain all the samples sequenced in one run. Consequently the relation is one sample sheet -> one run. Taking this into account: *Case Multiple Index Library in the same run: when you configure a run with projects that use different Index Library you must configure different sample sheets in IEM with each Index library used and merge them into one valid sample sheet before uploading it into iSkyLIMS.
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Special case Nextera XT: Nextera XT index library is configure in IEM as a complete library kit with all 320 possible index in all sets of Nextera XT (A,B,C and D). As BaseSpace only is able to configure 96 index plates for NextSeq, this complete library is not configured in BaseSpace. In order to solve this problem, you need to process this sample sheet the same way as they were different Index Library, with different projects.
- Create different sample sheets in IEM, one per each Index library. Each one with a different project Name
- Merge the sample sheets into one valid one with excell.
- Upload the file into iSkyLIMS, and in the second form fix the Index Library Name with the correct one for each project.
When all information was corrected, click on the submit button to get the third and the last page for NextSeq run creation.
- Third. This third screen has the propose to describe that the run creation process was correctly successful and it provides you the link of the file, in the right format, to upload it into BaseSpace.
