> For the complete documentation index, see [llms.txt](https://help.basespace.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.basespace.illumina.com/manage-data/import-data/fastq-upload-reqs.md). # FastQ Upload Requirements The FASTQ file is a text format file used to represent sequences. Each record has four lines of data: an identifier (read descriptor), the sequence, +, and the quality scores. For a detailed description of the FASTQ format, see [FASTQ Files](/files-used-by-basespace/fastq-files.md). Make sure the FASTQ file adheres to the following upload requirements: * FASTQ files are generated on Illumina instruments and saved in gzip format * The name of the FASTQ files conforms to the following convention: `SampleName_SampleNumber_Lane_Read_FlowCellIndex.fastq.gz` * Examples: `SampleName_S1_L001_R1_001.fastq.gz` `SampleName_S1_L001_R2_001.fastq.gz` * The read descriptor in the FASTQ files conforms to the following convention: `@Instrument:RunID:FlowCellID:Lane:Tile:X:Y ReadNum:FilterFlag:0:SampleNumber:` * Examples: Read 1 descriptor: `@M00900:62:000000000-A2CYG:1:1101:18016:2491 1:N:0:13` Corresponding Read 2 descriptor has ReadNum field: `@M00900:62:000000000-A2CYG:1:1101:18016:2491 2:N:0:13` Quality considerations: * The number of base calls for each read equals the number of quality scores. * The number of entries for Read 1 equals the number of entries for Read 2. * The uploader determines whether files are paired-end based on matching file names in which the only difference is the ReadNum. * For paired-end reads, read 1 and read 2 files need to be uploaded together or can be combined later. * Each read has passed filter. --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter: ``` GET https://help.basespace.illumina.com/manage-data/import-data/fastq-upload-reqs.md?ask=&goal= ``` `ask` is the immediate question: it should be specific, self-contained, and written in natural language. `goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.