FAQ

No, we are a Core Facility within the School of Biological Sciences at the University of Edinburgh. All staff are university employees.

We are an open-access academic facility, and are happy to work with researchers on a “fee for service” basis, or as a full collaborator. We are happy to provide just a quote for a piece of work where you know exactly what you want, or help you develop an idea and do the work in full collaboration. We pride ourselves on being able to engage with the entire research process, from project design, grant writing, project execution, data analysis and results write up (posters, papers, presentations etc).  Please get in touch through our Contact page and a member of our project team will contact you.

Please do contact us early in your experimental planning or grant writing process so that we can best help you write a successful application.

We provide a complete genomics service, from sample QC, through library production, sequencing/data collection, and data cleaning to in-depth analysis. We offer DNA and RNA sequencing on Illumina (NovaSeq and MiSeq), PacBio (Revio System), and Oxford nanopore Technologies (PromethION). We deliver data from a small RNA-seq projects through to multi-whole genome resequencing projects involving tens of Terabytes of data. Similarly our Bioinformatics support ranges from data QC through to management of major genome sequencing and analysis projects, and includes advanced training.

Edinburgh Genomics currently has three main areas of expertise: 

• Sequencing on MiSeq, NovaSeq 6000, Pacific Biosciences Revio, and Oxford Nanopore Technologies PromethION. Whether you want to sequence a bacterial genome, or the genome of a mammal; survey a microbiome to identify the species and genes present; count mRNAs, ncRNAs, smallRNAs; identify and score genetic variants; explore the epigenome of your study system; or perform the latest single cell sequencing, Edinburgh genomics can offer the appororiate technology.
• Bioinformatic analyses ranging from exacting data QC through to in-depth exploration of the genome biology of complex systems. We also offer advanced training in bioinformatics, including bespoke training for research groups.

Please fill in the enquiry form on our Contact page. Remember to tell us what your deadlines are, and please do give us as much information as you can about your needs. A member of our project team will contact you as soon possible to discuss the project in more depth and will develop a quotation to deliver to your project specifications. Please allow a week to 10 days for this process.

Please see our Sample Requirements page for information on sample preparation, sample QC and the amounts we need for different library preparation methods. If you have any questions, please contact the member of the project team you have been discussing your project with directly.

Please do contact us early in your experimental planning or grant writing process so that we can best help you write a successful application.

Edinburgh Genomics is a “cost recovery” facility: we must recover from the services we offer the full cost of delivering them. It is very hard to give simple guidelines for how much a sequencing experiment will cost. Suffice to say that Edinburgh Genomics prides itself for being not only high-throughput and high-quality, but also competitive on price. When you discuss your needs with our project team, we will indicate what our prices will be. Our large throughput means we can negotiate good deals from suppliers, especially if the reagents are all for one project. As we are a full cost recovery facility, it is hard for us to offer discount where the size of the project does not attract additional interest from suppliers.

We are required to charge VAT at a non-zero rate for projects with collaborators/customers outside the University of Edinburgh unless a formal collaboration agreement is in place. Do contact us to discuss this.

We use a secure system to deliver data back to collaborators. When your project data are ready for download, you will be contacted and given a link to your data. No-one else can see your data unless you give them access. 

We leave next generation sequencing data on our live website for one month after we have notified you, and guarantee to store the data securely on local discs for three months after notifying you it is ready. You can ask us to keep it for longer.

It is hard to give exact timings for every project in a general response to this question, but we aim to turn round samples as fast as we can, and to deliver analyses back to collaborators within an agreed timeline. When we set up a project with you we will give you an estimate of how long we expect it to take. For user supplied next generation libraries and small data volumes, turnaround can be fast (from 1-2 weeks). For larger projects involving hundreds of samples and terabases of data, obviously, turnaround is longer.

NERC has recently commissioned a new environmental omics facility (https://nerc.ukri.org/latest/news/nerc/13-million-investment-for-neof/). The new two node NERC Environmental Omics Facility (NEOF) is based at the Universities of Liverpool and Sheffield and replaces the current three node NERC Biomolecular Analysis Facility (NBAF) based at the Universities of Edinburgh, Liverpool and Sheffield. The general expectation is that most requests for genomic services for NERC research will now be directed to NEOF. Edinburgh Genomics remains open for business and continues to provide genomics services for research collaborators and customers across academia, government and industry. Edinburgh has played an active role in hundreds of NERC sequencing and bioinformatic projects over the past decade and while no longer formally providing services in this role the facility will continue to support NERC-area research however possible. If your research requires specific expertise, equipment or collaborators within Edinburgh Genomics or the University of Edinburgh please do get in touch before submitting NERC applications and we will discuss how we can help. We will also continue to deliver currently funded NERC research supported by the facility.

We try and keep our website as up to date as possible so you should find acurate information on our training page. If you don’t see a date next to your chosen course then you can register your interest in it here and we will get back to you via email as soon as a date is set. We usually run three or four iterations of each of our popular courses every year so if you just missed out don’t worry: a new itteration of the course will be running within a few months. Also, please do keep up with us on X where we often advertise our courses first!

We run our training sign-ups with an automated reply service which should send you a response to your sign-up almost instantly. This email, from edge-training@ed.ac.uk, often gets put in the junk folder so check there first. If you still haven’t got a confirmatory email then get in touch with us at edge-training@ed.ac.uk, it’s possible some thing has gone wrong. 

There are a number of ways in which you can pay for our courses after you have signed up via the link on the course page. Details will be sent to you in the automated confirmation email but in short:

• If you are based at The University of Edinburgh or the Roslin Institute and wish to pay from a grant, please provide your POETA codes in as much detail as possible as well as the PI’s name. 
• If you wish to pay by invoice, please respond with your company name, address, and purchase order number. Purchase Orders should be raised to “The University of Edinburgh.” If your institution is outwith the UK but within the EU, please include the VAT Reg Number. If you require a copy invoice by email, please state so explicitly.
• If you wish to pay from a personal bank account or using your credit or debit card, please use the provided ePay link for the course.
• Unfortunately, we cannot accept cash payments.

We don’t offer any bursaries for attendance at our courses as standard. We occasionally do get funing for staff/students working under specific funding bodies but we will let you know of these on sign-up if avaialble. There are a few external organisations that offer training grants for courses such as ours, for example, the Genetics Society which offers training bursaries for members. We have done our best to make our courses accessible through tiered pricing and we work on a cost-recovery model. 

Most of our courses are run on our own Edinburgh Genomics flavored virtual machines running on the Amazon Web Services (AWS) cloud. These machines come with all the necessary data and tools preinstalled all you have to do is connect.

To do this all you need is a Virtual Network Computing (VNC) viewer (or VNC ‘client’) that will connect your home machine to this cloud based virtual machine (VM). We recommend TigerVNC as its easy to use and works well. Download the latest version here: github.com/TigerVNC/tigervnc/releases 

Depending on what operating system you use you will need a different version of the “vncviewer-1.12.0” file: Windows users will need a .exe version, Mac users will need the .dmg version (and then drag the TigerVNC icon into your applications list), whilst Linux users can download the .tar.gz or .jar versions.

You can also use any other VNC viewer you please: MobaXterm, Remmina, RealVNC etc. but Tiger VNC will give you the best experience.

Our Intro to Python course uses a slightly different system, the details of which will be sent to you prior to the course via email.