illumina NextSeq 550Dx User Manual

Chapter 4 Scanning
Scanning
Introduction 27
Scanning Workflow 28
Download the DMAP Folder 28
Load the BeadChip Onto the Adapter 29
Set Up a Scan 30
Monitor Scan Progress 32
Introduction
To perform a scan on the NextSeq 550Dx instrument, you need the following run components:
u A hybridized and stained BeadChip
u The reusable BeadChip adapter
u Decode Map (DMAP) files for the BeadChip you are using
u A manifest file for the type of BeadChip you are using
u A cluster file for the type of BeadChip you are using
Output files are generated during the scan and then queued for transfer to the specified output folder.
Perform analysis using the BlueFuse Multi software, which requires that scanning data are available in a
genotype call (GTC) file format. By default, the NextSeq 550Dx instrument generates normalized data
and associated genotype calls in the format of a GTC file. Optionally, you can configure the instrument
to generate additional intensity data (IDAT) files. For more information, see BeadChip Scan
Configuration on page 51.
Decode File Client
The DMAP folder contains information that identifies bead locations on the BeadChip and quantifies the
signal associated with each bead. A DMAP folder is unique for each BeadChip barcode.
The Decode File Client Utility enables you to download DMAP folders directly from Illumina servers
using standard HTTP protocol.
For access to the Decode File Client, go to the Decode File Client support page on the Illumina website
(support.illumina.com/array/array_software/decode_file_client/downloads.html). Install the Decode File
Client on a computer with access to the network location of the DMAP folder.
For more information, see Download the DMAP Folder on page 28.
Manifest Files and Cluster Files
For each BeadChip, the software requires access to a manifest file and cluster file. Each manifest and
cluster file is unique to a BeadChip type. Make sure that you use cluster files that include NS550 in the
file name. These files are compatible with the NextSeq 550Dx system.
u Manifest file—Manifest files describe the SNP or probe content on a BeadChip. Manifest files use
the *.bpm file format.
u Cluster files—Cluster files describe the cluster positions for the Illumina genotyping array and are
used when analyzing data to make the genotype call. Cluster files use the *.egt file format.
The location of the files is specified on the BeadChip Scan Configuration screen. From the NCS Home
screen, select Manage Instrument, System Configuration, and then BeadChip Scan Configuration.
Document # 1000000041922 v01
For Research Use Only. Not for use in diagnostic procedures.
27

illumina NextSeq 550Dx Specifications

General

Brand	illumina
Model	NextSeq 550Dx
Category	Laboratory Equipment
Language	English