FASTQ File Format for Genome Sequencing Data

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FASTQ Format Compatibility

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FASTQ is a common format for genome sequencing data

FASTQ's can be uploaded with any commonly used file extension with or without compression:

  • .fastq
  • .fastq.gz
  • .fq
  • .fq.gz

 

The following types of FASTQ files are compatible with Sequencing.com:

  • Paired FASTQ
    • All genome data is contained within a total of two fastq files
      • The main part of the filename (before the extension) for both paired files must be exactly the same except for the R1 and R2 designations:
        • the filename of the file containing the forward sequence should include R1
          • Example: samplefastqfilename-R1.fastq.gz
        • the filename of the file containing the reverse sequence should include R2
          • Example: samplefastqfilename-R2.fastq.gz

 

The following types of FASTQ are not compatible:

  • Single read FASTQ file
  • Concatenated FASTQ file
  • Three or more FASTQ files for the same genome.
    • Example: If there are three or more paired fastq files for the same genome then the files will not be compatible.
    • Example: If there is one fastq file for each chromosome then these files will not be compatible.

 

If you were provided with a single read FASTQ file (just one fastq) or were provided with three or more files for a single genome, do not upload the files into your Sequencing.com account.

  • Sequencing.com may not be able to properly process these files.
    • If the files are uploaded, there may be issues properly processing the files. Known issues include:
      • The incorrect sex may be assigned to the file by Sequencing.com's Automatic Genetic Sex Determination.
      • If the files are processed using apps, the app results may be incorrect.
  • Contact the laboratory or company that provided your genome data and request that they provide your data as 'Paired FASTQ files' (you'll receive two files) or 'A Single Concatenate FASTQ file' (you'll receive one file).
    • Paired FASTQ and a single concatenate FASTQ are the most common types of raw data files generated by whole genome sequencing and exome sequencing when the sequencing is performed for healthcare professionals or consumers.

 

If you are unable to obtain the paired FASTQ:*

  1. Concatenate all of the individual fastq files into paired fastq (R1 and R2).
    • For paired fastq files please ensure the main part of the filename (before the extension) is exactly the same except for the R1 and R2 designations:
      • the filename of the file containing the forward sequence should include R1
        • Example: samplefastqfilename-R1.fastq.qz
      • the filename of the file containing the reverse sequence should include R2
        • Example: samplefastqfilename-R1.fastq.qz
  2. Upload the paired fastq files into your Sequencing.com account using Big Yotta File Uploader.

 

*Combining three or more FASTQ files into paired FASTQ requires bioinformatics expertise. This is a complex task and should only be performed by a bioinformatician or genomics professional.