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How to remove a BCL file from analysis in MiSeq Reporter or Local Run Manager

Background: In situations where a single BCL file is corrupted or displays a high error rate, it is possible to remove the affected BCL from secondary analysis. This removes the affected tile at the impacted cycle from all downstream analysis.
  1. 1.
    On MiSeq, open D:\Illumina\MiSeqAnalysis<run folder>\Data\Intensities\BaseCalls\L001
  2. 2.
    Open the folder for the affected cycle of the run.
  3. 3.
    Locate the BCL file for the affected flow cell tile.a. For example, for tile 2103, the BCL file name is s_1_2103.bcl 4. Append .bak to the BCL file name.a. For example, s_1_2103.bcl.bak 5. Requeue analysis of the run to repeat analysis with the problematic BCL file excluded from the results. For all of the clusters on the affected tile in the affected cycle, the base calls will be replaced with an N (no call).
For any feedback or questions regarding this article (Illumina Knowledge Article #2415), contact Illumina Technical Support [email protected].
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