Bioinformatic consultancy covering experimental planning to data analysis is available in three main areas: RNA sequencing (bulk and single cell), variant calling from DNA sequencing, and a specific application of identifying endogenous Avian Leukosis Viruses in bird genomes (with skills transferable to other ERVs and species). Andrew is also able to offer bespoke analysis of other sequencing types (e.g. ChIPseq, ATACseq) - just get in touch to discuss your project.
RNAseq
- Experimental setup: bulk vs single-cell
- Power analysis
- Sample processing and sequencing submission
- Data QC
- Alignment and quantification
- Differential expression analysis
- Gene set enrichment analysis
- Unsupervised clustering
- Data interpretation
- Data upload for sharing and open access
Variant calling from WGS/WXS
- Experimental setup: depth, sample pairing, short vs long read
- Sample processing and sequencing submission
- Data QC
- Alignment, adjustments and variant calling
- Variant effect prediction
- Mutational signature analysis
- Sliding window analyses, assessment of non-random distributions
- Driver gene identification
- Structural variant analyses
- Data interpretation
- Data upload for sharing and open access
ALVE characterisation
- Genotyping vs de novo identification
- Diagnostic assay design
- ALVE detection likelihood
- Experimental setup and sequencing strategy
- Sample processing and sequencing submission
- Data QC
- Alignment and ALVE identification
- TVB genotyping
Across various academic and commercial projects, Andrew is well-versed in handling confidential and commercially sensitive data. All discussions, documents and data will be privileged, and stored on dedicated, password-protected filestores.
Please contact Andrew for more information, rates and availability.