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:

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FASTQ files are generated on Illumina instruments and saved in gzip format

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The name of the FASTQ files conforms to the following convention:

SampleName_SampleNumber_Lane_Read_FlowCellIndex.fastq.gz

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The read descriptor in the FASTQ files conforms to the following convention:

@Instrument:RunID:FlowCellID:Lane:Tile:X:Y ReadNum:FilterFlag:0:SampleNumber:

Quality considerations:

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The number of base calls for each read equals the number of quality scores.

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The number of entries for Read 1 equals the number of entries for Read 2.

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The uploader determines whether files are paired-end based on matching file names in which the only difference is the ReadNum.

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For paired-end reads, read 1 and read 2 files need to be uploaded together or can be combined later.

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Each read has passed filter.