# 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](https://help.basespace.illumina.com/files-used-by-basespace/fastq-files).

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.