Bases2Fastq generates FASTQ files using the naming convention "SampleName_Read.fastq.gz". Use --legacy-fastq to apply a legacy file naming convention to FASTQ files, such as "SampleName_S1_L001_R1_001.fastq.gz". Certain bioinformatic tools (e.g. Cell Ranger from 10x Genomics) might require this naming convention.
When would I use the “--legacy-fastq” bases2fastq option?
For more information, reach out to your Field Applications Scientist or Element Biosciences Support at support@elembio.com.
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