How to analyze an incomplete run using BCL Convert

Background

If a run aborts prematurely before finishing all cycles, the data can still be salvaged using the BCL Convert application in BaseSpace or locally on instrument based on the following factors:

• The index sequences must be unique from sample to sample.

  • Ideally, the run stopped after completing the index reads. However, data can still be generated as long as indexes are unique, albeit with the possibility of quality concerns due to smaller hamming distances.

• If the run stopped before completing the index reads, it is not possible to demultiplex and identify samples and data cannot be obtained.

To generate FASTQs with BCL Convert:

1. Determine the last cycle sequenced.

2. Create a new v2 sample sheet and use the OverrideCycles setting to mask the un-sequenced cycles using "N".

   1. For example, if a run was set up as 151|8|8|151 and the last cycle sequenced was 177, set OverrideCycles to 151;I8;I8;Y10N141.

   2. For more information, see How to use the 'OverrideCycles' setting in the Run Planning User Interface.

3. If the run aborted during the index cycles, use the OverrideCycles setting to mask the un-sequenced cycles using "N" and edit the sample sheet to remove the bases of the index that were not sequenced.

   1. For example, if a run was set up as 151|8|8|151 and the last cycle sequenced was 162, set OverrideCycles to 151;I8;I3N5;N151 and remove the last 5 bases from the index2 column in the sample sheet.

4. Upload the new sample sheet to a Project if using the BCL Convert app in BaseSpace.

5. Requeue analysis using BCL Convert.

For any feedback or questions regarding this article (Illumina Knowledge Article #5949), contact Illumina Technical Support [email protected].