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