September 2019

Differential Gene Expression Analysis Workflow


QC of aligned reads

  • Alignment Rate
  • Duplication Rate
  • Genomic location of reads
  • Transcript coverage

QC of aligned reads - Alignment Rate

  • Depends on:
    • Quality of Reference Genome
    • Quality of library prep and sequencing
    • For human and mouse > 95%

QC of aligned reads - Duplication Rate

  • Human exome is ~30 Mb therefore there are < 30 million possible reads
  • Duplication rates in RNAseq can be > 40%

QC of aligned reads - Genomic location of reads


QC of aligned reads - Transcript coverage