Fix My Sample Sheet

BaseSpace now has a sample sheet fix feature. This feature addresses the issue where the user has started a run on the MiSeq with a sample sheet that has a reference genome that is either referenced by an invalid path or is not support by MiSeq or BaseSpace.

In the event that the user has an invalid genome parameter in the sample sheet, the run will still continue. The data will still be copied over to BaseSpace, however, the analysis will not be kicked off until the user fixes the issue with the sample sheet.

Let’s run through a scenario below:

I am a user that has started a run on Miseq. My run is kicked off, however, my genome path in my sample sheet is not valid for some of my samples.

When I log into BaseSpace to check on my run, I will see in my run summary that the analysis is no available and the run is in need of attention. A message “The Sample Sheet Needs Attention” appears on my summary. I am also presented with a button which allows me to “fix sample sheet”


Upon selecting “Fix Sample Sheet” I am presented with the BaseSpace Fix Sample Sheet window. In this window I am presented with the run details, an explanation of the sample sheet issues, as well as a table identify the samples with incorrect genomes.

The Sample sheet Issues box gives me a brief explanation of the issues along with the number of samples that need my attention.


To correct the issue, I must assign the appropriate genome to the samples below that have been identified as error; with a red genome path. I simply do this by selecting a sample, and then selecting a genome. I also have the option to only see error samples or to multi select samples that may all use the same genome.


Once I select the sample(s) that I want to choose a genome for, I click on the drop box and select a genome from the list of compatible genomes available in BaseSpace.


Once I click apply, the genome selected is applied to the samples that I have selected and the table is updated. The Sample Sheet Issues box will display how many remaining samples still need my attention. If all samples have a valid genome, the queue analysis option will appear.


Once I click Queue Analysis, a message will appear that my sample sheet has been updated and my analysis has been queued.


If I choose to leave the page prior to re-queuing my analysis, I will be presented with a message that my sample sheet issues have no been resolved and my analysis will not start.

With the Sample Sheet Fix feature BaseSpace will make catching sample sheet errors easier, and help you get your analysis done faster. We intend on adding more functionality to this feature and help you make your analysis easier, faster, and error free. Please let us know how you use this feature, and feel free to suggest new ways of making your sample sheet validation and analysis easier.

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