Can I convert BCL files to FASTQ files?

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BCL files contain raw image files. In most cases, they are automatically converted to FASTQ files on Illumina instruments once the sequencing run is complete.

Converting BCL files to FASTQ files should be a standard analysis step on all Illumina sequencing instruments. The procedure doesn’t differ between bulk and single-cell data, and standard guidelines can be followed.

Refer to the bcl2fastq Conversion User Guide for additional information.

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