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  • 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
  • Analysis Results
    • Accessing Results
    • DRAGEN Report
      • Single-Cell RNA
      • Trimmer
      • DRAGEN FastQC
      • Mapping
    • Secondary Analysis Results
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  1. Analysis Methods

FASTQ Processing

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Last updated 3 months ago

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For data processed with the Illumina Single Cell 3’ RNA Prep Kit, each read in R1 includes a 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.