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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 Results
  2. DRAGEN Report

DRAGEN FastQC

DRAGEN FASTQC Plots

Plot
Description

Base Quality by Position

Phred-scale quality value for bases at a given location

Mean Base Quality by Position

Average Phred-scale quality value of bases with a specific nucleotide and at a given location in the read

Read Length Distribution

Total number of reads with each observed length

Read Quality Distribution

Total number of reads with each observed average Phred-scale quality score

%GC Content

Percentage of sequences with each GC content across the whole length of each sequence compared to a modelled normal distribution of GC content

Read Quality by %GC Content

Average Phred-scale read mean quality for reads with each GC content percentile between 0% and 100%

Ambiguous Base Content by Position

Percent ambiguous bases at a given location

Base Content by Position

Percent of bases of each specific nucleotide at given locations in the read

Adapter Content by Position

Percentage of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length increases

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Last updated 4 months ago

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