> For the complete documentation index, see [llms.txt](https://knowledge.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://knowledge.illumina.com/software/dragen/software-dragen-faq-list/000006031.md).

# How to enable DRAGEN to process multiple FASTQ files for the same subject?

**How to enable DRAGEN to process multiple FASTQ files, produced by the Illumina bcl2fastq or BCL Convert programs, for the same subject?**

The command line options, combine-samples-by-name or fastq-list, can be used for this purpose. Both options are specified in the User Guide. The fastq-list is the preferred option, which will let you specify all FASTQ files for a sample along with read group IDs. The fastq-list is in CSV format and can include all the samples in a flowcell/run (See the [FASTQ List documentation](https://help.dragen.illumina.com/product-guide/dragen-v4.4/bcl-conversion#fastq-list-output-file) for more information about FASTQ List format).

To process a specific sample from the CSV file, use the --fastq-list-sample-id {SampleID} option. Only the entries in the fastq-list file with an RGSM value matching the specified SampleID are processed. If using DRAGEN BCL conversion, then the conversion process will also generate these fastq-list CSV for you.

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| *For any feedback or questions regarding this article (Illumina Knowledge Article #6031), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000006031%20-%20Software%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


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