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Standardised Analysis Pipelines

The SAGC supports high-throughput sequencing conducted through the facility by providing a range of best practise analysis pipelines that are available to be run on different projects. These include:

  • Whole Genome/Exome variant calling: High-throughput sequencing quality control, alignment, small and large germline variant and copy number variant detection
  • Cancer variant detection: Identification of germline and somatic variants, copy number variations and gene fusion detection
  • Gene expression (RNA-seq): Transcriptome profiling of RNA samples using alignment and gene quantification methods
  • DNA methylation (WGBS/RRBS/MeDIP): DNA methylation calling from bisulfite and restriction enzyme digest methods
  • Other Epigenomics and Chromosome Conformation Capture (3C) analyses (ChIP/ATAC-seq etc): Chromatin accessibility and protein binding profile assays for the analysis of Transcription Factors, Histone Modifications and physical interaction information.