Knowledge Center

FASTQ Format Compatibility

Fastq file compatibility for whole genome sequencing data 

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

  • A whole genome or exome genome is provided as two fastq files known as 'paired 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

Multi-FASTQ (only when automatically imported)

  • A whole genome is provided as four or more fastq files.
    • Some sequencing laboratories may provide a genome as four or more fastq files. For example, a lab may provide a genome as 12 different fastq files while another lab may provide a genome as 18 different fastq files.
    • While the optimal way to provide a genome is as a paired fastq (two fastq files), Sequencing.com is compatible with genomes provided as multi-fastq as long as the multi-fastq are directly imported from your account at the laboratory to your account at Sequencing.com.
      • For example, if your whole genome from Dante Labs was provided as 8 different fastq files then your genome is a 'multi-fastq' genome. It will be compatible with Sequencing.com as long as you use our automatic importer, which is an automatic transfer service that will import files directly from your Dante Labs account into your Sequencing.com account.
        • To use the automatic importer, go to the Upload Center and click the name of your test provider.
        • If your test provider is not listed, use Big Yotta to upload your BAM file.
  • Multi-fastq files uploaded by any other method, such as using Big Yotta or imported from a cloud provider, such as Dropbox or AWS, will not be compatible with Sequencing.com.
    • If you are unable to use the automatic importer, please upload your BAM file using Big Yotta. Your BAM file is an excellent file to use with apps. Learn more

The following types of FASTQ are not compatible:

Single read FASTQ file

Concatenated FASTQ file

Multi-FASTQ genomes (three or more FASTQ files for the same genome) when the automatic importer is not used

  • Example: If there are three or more paired fastq files for the same genome then the files will not be compatible unless they are imported into your account using the automatic importer at the Upload Center.
  • Example: If there is one fastq file for each chromosome then these files will not be compatible. Please ask your laboratory to provide your genome as a paired fastq (two fastq files).

 

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.

 

Related

Guide to understanding and using Whole Genome Sequencing data files