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Quality Control

Quality control (QC) is the first step in any RNA-seq workflow. NotchBio automatically generates QC reports for your uploaded FASTQ files.

Running QC

Section titled “Running QC”
  1. Navigate to your project → Run tab
  2. QC runs automatically when you start the pipeline
  3. Results show per-sample quality metrics

Key Metrics

Section titled “Key Metrics”
  • Total reads — Number of sequencing reads in the file
  • Q30 rate — Percentage of bases with quality score ≥ 30
  • GC content — Distribution of G and C nucleotides
  • Sequence length — Distribution of read lengths
  • Adapter content — Presence of sequencing adapters

Interpreting Results

Section titled “Interpreting Results”
  • Good quality: Q30 > 85%, even GC distribution, minimal adapter contamination
  • Needs attention: Q30 < 80%, biased GC distribution, significant adapter presence
  • Action: If quality is low, adjust preprocessing parameters