FASTQ Files

Read 1, Read 2, and Index Read 2 sequencing files

For either the Seven Bridges Genomics platform or local pipeline installation, first obtain sequence FASTQ files: Read 1 and Read 2. For ATAC-Seq assays, also obtain Index Read 2. Although the FASTQ filenames can have any format, we recommend the following:

  • Include R1, R2, or I2
  • The base name should be the same for R1, R2 and I2
  • Convert uncompressed files to .gz format

Example library FASTQ files for WTA assay:

  • WTALibrary1_S1_L001_R1_001.fastq.gz
  • WTALibrary1_S1_L001_R2_001.fastq.gz

Example library FASTQ files for ATAC-Seq assay:

  • ATACLibrary_S2_L001_R1_001.fastq.gz
  • ATACLibrary_S2_L001_R2_001.fastq.gz
  • ATACLibrary_S2_L001_I2_001.fastq.gz

Do not use special characters or spaces in the filenames, or the analysis might fail. Use only letters, numbers, underscores, or hyphens.

Note: If you are downloading the files from BaseSpace, follow these steps:

  1. Choose the run to download in BaseSpace
  2. Click the download icon on the main screen
  3. If necessary, install the BaseSpace downloading application
  4. Click Select all fastq files for this run
  5. Download the files. This might take several minutes

For more information, go to help.basespace.illumina.com.