FASTQ File 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.
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
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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:
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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. |