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.

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.

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