How should I demultiplex my NextSeq run in order to analyze my data on Archer Analysis

NextSeq demultiplexing should be done using Illumina's bcl2fastq2 Conversion Software.

Observe the following:

  • Be sure to use the "--no-lane-splitting" option mentioned on page 28 of the Illumina's bcl2fastq2 Conversion Software v2.17 Guide. The default output from the software splits the data by lane for each sample, resulting in four sets of fastq files (one for each lane) per sample. A single set of fastq files is required for each sample uploaded to Archer Analysis. Therefore, using the "--no-lane-splitting" option is critical.
  • Note that Archer Analysis has the ability to automatically process demultiplexed sequencer data through the Watched Folders mechanism. Since every sequencing environment is different, you will need to provide a small linker script which copies your paired fastq files to the location(s) specified for the Watched Folder(s). Your Archer representative can help you with more details.
  • The reverse complement of the P5 adapter sequences provided by Archer are needed to successfully demultiplex the NextSeq run.

Download Archer adapter sequences and their reverse complements file here.


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For Research Use Only. Not for use in diagnostic procedures. For Research Use Only. Not for use in diagnostic procedures.