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Why are underscores in sample names changed to dashes in the FASTQ file names?

Any underscores in Sample ID and Sample Names are converted to dashes to preserve sample naming conventions for downstream analysis. Illumina FASTQs use the following format: SampleName_SampleNumber_Lane_Read_FlowCellIndex.fastq.gz
Local Run Manager, MiSeq Reporter, bcl2fastq, and BCL Convert when used through BaseSpace Sequence Hub (BSSH) will make this change. However, locally-run BCL Convert, locally-run bcl2fastq, and onboard analysis on the NovaSeq X and NextSeq 1000/2000 will keep underscores as input.
Additionally, note that FASTQs with underscores in the SampleName field cannot be uploaded to BSSH; any underscores in sample names must be converted to dashes or removed prior to upload.
For any feedback or questions regarding this article (Illumina Knowledge Article #3636), contact Illumina Technical Support [email protected].
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