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When sequencing runs are finished, we automatically upload FastQ files to a client’s Box.com account.

These files are typically found in the directory:

  • ClientName->Reports->ReportID->FastQ

The FastQ files in this directory use the following naming convention:

  • ClientName_ProjectID_SampleID_SampleName_sometext_R1_sometext.fastq.gz
  • ClientName_ProjectID_SampleID_SampleName_sometext_R2_sometext.fastq.gz


  • ClientName = the name of the client’s organization
  • ProjectID = a SeqCenter internal project identifier (you can generally ignore this)
  • SampleID = a SeqCenter internal sample identifier (you can generally ignore this)
  • SampleName = this is the sample name supplied to the Sequencing Center by the client; it typically corresponds to the sample vial name
  • sometext = a text string added by the sequencer (you can ignore this)
  • R1 = the forward read identifier
  • R2 = the reverse read identifier
  • fastq = identifies this as a file in FastQ format
  • gz = the files are compressed in gzip (“.gz”) format


In most, but not all, sequencing runs we use paired-end reads.  In this format there is a forward read, “R1”, and a reverse read, “R2”, which together form a single paired-end read. The forward reads and reverse reads are stored in separate files.  Many bioinformatics applications process these two files together, so you can keep track of them with the “R1” and “R2” identifiers.