Expertise offered by the Sheffield Bioinformatics Core

The SBC has expertise in the following areas, and software packages:-

Experimental Design

If you are planning an experiment, please come to us before generating data so that we can discuss the design

The Core is experienced in advising on the following issues:-

  • Optimal number of replicates
  • Biases and confounding factors
  • Single-end or paired-end sequencing
  • Depth of sequencing required
  • Contacts at Sequencing vendors

Next Generation Sequencing (NGS) Analysis

  • BWA, and other aligners for all NGS platforms and applications
  • edgeR, DESeq2, STAR and salmon (among others) for RNA-Seq analysis
  • GATK, VarScan and MuTect for somatic and germline mutation calling
  • MACS2, and other peak callers for ChIP-Seq and ATAC-seq analysis
  • Analysis of public datasets on Gene Expression Omnibus (GEO) and Sequencing Read Archive (SRA)

Downstream Analysis

  • Downstream analysis of gene lists to identify over-represented pathways / ontologies using GSEA, goseq, or other online tools such as DAVID or Genetrail.

Single Cell RNA-Seq

  • QC, analysis and visualisation for single cell RNA-seq data
  • Analysis of Spatial transcriptomics data

Microarray Analysis

  • Experience with data from Affymetrix and Illumina platforms
  • Varying data types, including expression, methylation (450K), SNP and copy-number

Further Expertise

  • Custom visualisation of high-throughput data
  • Custom bioinformatic workflows and piplines with nextflow
  • Packaging and deploying software environments with docker
  • Data Management and curation
  • Creating interactive web applications wih shiny

As well as these analysis services, we also provide training courses and bespoke 1-to-1 training for researchers

For experimental advice on performing high-throughput studies, please contact the SITraN multi-omics facility