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DRAGEN Single Cell RNA
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DRAGEN Single Cell RNA
  • Introduction
  • Get Started
    • Prerequisites
  • Run Set Up
    • Sample Sheet Introduction
    • Run Planning in BaseSpace Sequence Hub
    • Sample Sheet Requirements
    • Manual Launch on BaseSpace
  • Analysis Methods
    • FASTQ Processing
    • Error Correction
    • Transcript Counting
    • PIPseq CRISPR Mode
  • Analysis Results
    • Accessing Results
    • DRAGEN Report
      • Single-Cell RNA
      • Single-Cell Clustering
      • Trimmer
      • DRAGEN FastQC
      • Mapping
    • Secondary Analysis Results
  • Tertiary Analysis
    • Illumina Connected Multiomics
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  1. Analysis Methods

FASTQ Processing

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Last updated 6 days ago

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For data processed with the Illumina Single Cell 3’ RNA Prep Kit, each read in R1 includes a cellular barcode sequence followed by a 3-base binning index (BI) sequence. R2 includes the sequences cDNA constructs created from the captured mRNA, which contain random cut sites that serve as intrinsic molecular identifiers (IMIs) and are used for molecular counting.

For more information about FASTQ processing refer to the detailing the DRAGEN PIPseq scRNA Pipeline.

DRAGEN documentation