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Centre for Genome-Enabled Biology and Medicine

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Services

We provide a range of services including consultation, planning, analysis and training. In all cases, the initial consultation is free but, thereafter, it is necessary for us to make a charge. Advice to PhD students is, however, free, although limited time is available for this.

We recommend that you and contact us to arrange an appointment to discuss your needs or to send an initial enquiry with details of study design, sample numbers and primary aims/research question. Appointments are available at Old Aberdeen or Foresterhill.

If you wish to be provided with a bioinformatics service, after this initial enquiry, please complete and return the Service Request Form .

Consultation

If you are considering a project, or have a bioinformatics problem you wish to ask advice on, we are happy to provide consultations. We make no charge for an initial consultation.

Planning

Assistance with planning the bioinformatics component of projects and in preparing grant applications is available. We recommend that people contact us as early as possible when planning a project.

Analysis

We provide data analysis for a range of projects using sequence data and also offer custom solutions requiring command line, HPC and/or biological informatics expertise. If you would like us to analyse data, please contact us to discuss your requirements or see below for more information.

Training

Training sessions are provided throughout the academic year for researchers at all positions. Topics covered include an introduction to Unix and Maxwell as well as analysis specific workshops.

Bioinformatics Analysis Services

The CGEBM Bioinformatics team provides comprehensive analytical support for a wide range of genomics applications and 'big data' informatics. A complete end-to-end solution, partial analytical workflows or single step support can be provided depending on your requirements. Typical timescales for our most common applications with straightforward designs and research questions are detailed below. Please discuss your requirements with the team to confirm the timescales required to deliver your research questions, as more complex designs or outputs and discovery driven iterative systems analyses will extend the analytical workflows.

The CGEBM team utilise the University of Aberdeen high performance computer cluster (HPC), Maxwell, for the processing power required for these analyses.


*Before starting work on a project, we will provide you with a quote, detailing what we will provide, costs and expected times, and a copy of our data policy.

We strongly recommend that you contact us when planning your project, if you wish us to perform data analysis. If you have not obtained our agreement at the planning stage, and insufficient resources have been allocated, we may not be able to fully analyse your data.

Differential Gene Expression: RNA-seq DEG

Comprehensive service typically 4-8 weeks:

  1. QC of data, alignment to reference and list of differentially expressed genes (DEG) using pre-defined statistical/filtering thresholds.
  2. More in depth statistical analysis (e.g. GLM) to reduce false negatives.
  3. Gene function analysis and systems biology: e.g. gene ontology, pathway and network mapping.
  4. OPTIONAL: Iterative biology drive analysis following initial discovery phase.
  5. Publication quality visualisation and reporting.
  6. Input to publication, including revisions and resubmissions.
RNA-Seq for de novo Transcriptome Assembly

Comprehensive service typically 8-26 weeks:

  1. QC of data.
  2. OPTIONAL: Removal of contamination reads e.g. from host.
  3. Assembly:
    1. Assembly with different assembler tools.
    2. Assembly metrics and comparisons. Selection of best assembly.
  4. Annotation of assembly:
    1. Annotation with Trinotate.
    2. Comparison to closely related species.
  5. OPTIONAL: Iterative biology drive, in depth annotation of specific loci of interest.
  6. Publication quality visualisation and reporting.
  7. Input to publication, including revisions and resubmissions.
Variant Calling, Annotation and Association Analyses

Comprehensive service typically 6-26 weeks:

  1. QC of data.
  2. Alignment to reference:
    1. Good quality reference that is the same species/strain as your experimental samples.
    2. Reference is poor quality and/or is a different strain to the experimental samples.
  3. Variant calling and filtering.
  4. OPTIONAL: Variant effect prediction, variant annotation and refinement of candidates.
  5. OPTIONAL: Association analyses.
  6. Publication quality visualisation and reporting.
  7. Input to publication, including revisions and resubmissions.
De Novo Genome Assembly

Comprehensive service typically 4-26 weeks:

  1. QC of data.
  2. OPTIONAL: Removal of contamination reads e.g. from host.
  3. Assembly:
    1. Assembly with different assembler tools.
    2. Comparison of assembly metrics. Selection of best assembly.
    3. OPTIONAL: Contamination checking and removal of contaminating contigs.
  4. Scaffolding to produce a more contiguous assembly.
  5. Gene Calling and annotation.
  6. OPTIONAL: Iterative biology driven, in depth annotation of specific loci of interest.
  7. Publication quality visualisation and reporting.
  8. Input to publication, including revisions and resubmissions.
Microbiome Analysis: 16S or ITS

Comprehensive service typically 4-8 weeks:

  1. QC of data.
  2. Denoise data with DADA2 to produce sequence variants with taxonomic assignments.
  3. Basic diversity analysis:
    1. Rarefaction analysis.
    2. Alpha diversity analysis.
    3. Beta diversity analysis.
    4. Taxa analysis including appropriate differential abundance testing.
  4. OPTIONAL: Extended analyses:
    1. Accuracy evaluation with mock community control.
    2. Predict metagenomic functional content and analysis.
  5. Publication quality visualisation and reporting.
  6. Input to publication, including revisions and resubmissions.
BIS-Seq: Methylation Calling and BIS-RNA-Seq

BIS-Seq: Methylation Calling

Comprehensive service typically 4-20 weeks:

  1. QC of data.
  2. Alignment to reference, methylation calling of bisulphite-treated samples and generation of raw methylation results/standard reports per strand and methylation context:
    1. OPTIONAL: Consolidation of raw methylation results into user-defined reports for subsequent downstream analysis.
    2. OPTIONAL: Alignment to reference (good quality reference), variant calling and filtering of non-bisulphite treated samples.
  3. Publication quality visualisation and reporting.
  4. Input to publication, including revisions and resubmissions.

BIS-RNA-Seq

Comprehensive service typically 10-24 weeks:

  1. QC of data.
  2. Alignment to reference, methylation calling of bisulphite-treated samples and generation of raw methylation results/standard reports per strand and methylation context (2 weeks):
    1. OPTIONAL: Consolidation of raw methylation results into user-definied reports for subsequent downstream analysis.
    2. OPTIONAL: Alignment to reference (good quality reference), variant calling and filtering of non-bisulphite-treated samples.
  3. Differential methylation analysis and reporting:
    1. OPTIONAL: Annotation of most significantly differentially methylated transcripts.
  4. Publication quality visualisation and reporting.
  5. Input to publication, including revisions and resubmissions.
Bar-Seq

Comprehensive service typically 4-8 weeks:

  1. QC of data.
  2. Barcode detection, counting and binning.
  3. Publication quality visualisation and reporting.
  4. Input to publication, including revisions and resubmissions.
ChIP-seq

Please discuss your design and aims with us to determine bioinformatics time required. Typically 8-14 weeks for comprehensive analysis of straightforward design:

  1. QC of data.
  2. Alignment to reference:
    1. Good quality reference that is the same species/strain as your experimental samples.
    2. Reference is poor quality and/or is a different strain to the experimental samples.
  3. Peak calling and QC of results.
  4. Peak annotation and motif analysis.
  5. Publication quality visualisation and reporting.
  6. Input to publication, including revisions and resubmissions.
Novel Applications / 'Big Data' Informatics

Custom informatics solutions can be developed for novel applications in genomics or for analysis of other types of 'big data', through integration of custom scripts with existing open source tools. Please discuss with the team who will evaluate your requirements and provide a proposed bespoke informatics solution and associated timelines.

Established Pipelines

Please enquire if you have an established pipeline that you lack the time, expertise or computer power to run yourselves and we can provide details of timescales and costs for implementing and running the pipeline to analyse your data.