Expertise
Staff in the Bioinformatics Support Unit have extensive expertise in the following areas of analysis. Get in touch to find out more.
Experimental Design
If you are planning an experiment, please discuss it with us before generating the data so that we can discuss the design.
In the BSU, we have extensive experience and can offer advice on the following issues:
- Statistical power and sample size
- Batch effects and other confounding factors, and how to deal with them
- Type of sequencing (platform, single or paired end etc)
- Sequencing depth
High Throughput Sequence Analysis
- BWA, Bowtie and other aligners for all NGS platforms and applications
- Mira, Velvet and SPAdes for de novo assembly, including HGAP for PacBio data
- STAR, Salmon, DESeq2, Limma and Trinity (among others) for RNA-Seq analysis
- Single-cell analysis with Seurat, Monocle and more
- GATK, VarScan and MuTect for variant calling
- MACS, SISSRs and other peak callers for ChIP-Seq analysis
- Bismark for bisulphite sequencing
- Kraken and QIIME for metagenomics sequence classification
- R-The R Project for Statistical Computing
- Bioconductor - Open source software for Bioinformatics
- CellRanger - 10x Genomics software
- SpaceRanger - 10x Genomics software
- Seurat - A computational strategy for single-cell RNA-seq data analysis
- Mutect2 - Call somatic SNVs and indels via local assembly of haplotypes
- epi2me - Oxford Nanopore Technologies data analysis
- SMRT - PacBio data analysis
Microarray Analysis
- Experience with data from all major array platforms (Affymetrix, Illumina, Nimblegen & Agilent)
- Varying data types, including expression, methylation (450K, 850K EPIC), MEDIP-ChIP, and tiling arrays
- BioConductor/R
- Affymetrix Transciptome Console
Proteomics Analysis
- Bioinformatic screening for potential protein-protein interactions
- Analysis of SILAC data using MaxQuant
- 2D-GE analysis
- Analysis of MS-SWATH data
Further Expertise
- Visualisation of high throughput data
- Database design
- Custom pipeline creation
- Custom software engineering
- Data management and curation - including repository deposition of high throughput data sets
- Remote homology and domain detection using HMMs
- We also provide training courses and bespoke 1-to-1 training for researchers and industry.
Equipment
The BSU have several powerful server solutions for work requiring more computational power with machines from 4 to 80 CPUs and 1 GPU, with 32GB to 380GB of RAM and several terabytes of associated storage.
An SFTP server to facilitate transfer of data and results.
The unit also makes extensive use of Newcastle Universities Rocket HPC Service.