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CIGC FAQ

Lab FAQ:

How much do genomics core services cost?

Pricing is available on request, please .

Can I access the Genomics core if I'm not from the Institute?

We are not a commercial facility, therefore our services are not normally available outside of the Institute and rarely outside University of Cambridge. The following further restrictions apply:

  • Library Preparation, Experimental Design Services and Equipment: these services are only available to researchers within the CRUK-CI except in exceptional circumstances
  • Next Generation Sequencing: Our NGS service is available for several University institutes & departments (see here for a full list). Sometimes we have spare capacity and can offer sequencing to other researchers within the University of Cambridge. If you would like to request one-off sequencing, please .

How do I get out of hours access?

Please and we'll get security to add access to your card.

How can I book equipment?

You need an account on Resource Scheduler from IT then ask us for training and access to specific equipment. When you're ready just and ask us for what you need.

What equipment does the genomics core have?

Take a look at our services dropdown list in the menu bar, or jump straight to a list of our equipment.

Do you offer any training?

We can train users on qPCR, Covaris and Bioanalyser generally on Thursdays 2-3pm but you do need to book one week in advance by . We don't find that training more than three people is very effective so sometimes there can be a waiting list. If you have any other training requests send them to us via too.

Training is required for the Covaris, Bioanalyser and QuantStudio. Please do let us know if you just want a refresher.

Should I acknowledge your work on my project?

Yes! Acknowledgements are one of the criteria used to judge the success of our core facility. If we did sequencing or library preparation for you, please acknowledge us in any papers you produce using that data. See our list of publications page for some suggested text.

NGS FAQ:

Do you QC my data?

Yes, we run every single lane through several QC tools including the MGA tool published by the Genomics and Bioinformatics cores. We use this QC to alert us to issues on the machines, but also to problems in user libarry prep.

What are your submission requirements?

Take a look at our submission guidelines page. If you are unsure do check with us as issues with submissions are likely to delay your project.

How do I submit samples to Genomics?

Take a look at our submission guidelines page. If you are unsure do check with us as issues with submissions are likely to delay your project.

What happens if the sequencing run fails?

Very few runs fail! However if your sequencing does go wrong because of a technical problem (instrument or chemistry) or if we're responsible, then you will not be billed, and we will rerun your sample. If the failure is due to the library then you will still be billed. We recommend a single lane of seqeuncing in the first instance if you have more than 3 or 4 lanes in total, this gives us a chance to QC everything.

How should I pool my libraries for NGS?

If your libraries are multiplexed you are required to pool them prior to submission. Our submission guidelines refer to the total quantity of library in your pool not to each index in your pool. So for example if we ask for a library at 10nM and you have five libraries, the final pool you provide to us will contain each library at 2nM but all libraries measured together are at 10nM.

A simple method to pool libraries:

1)     Quantify (using KAPA) and QC (using Bioanalyser) all of your libraries

2)     Select a concentration for pooling, often the lowest concentration of your library set. This should be above our submission guidelines.

3)     Dilute all of your libraries to be pooled to that concentration. Use Illumina Resuspension Buffer, EB, or Library Dilution Buffer (10mM Tris pH 8.5 with 0.1% Tween, available from CIGC).

4)     Combine an equal volume of all of your libraries in your pool tube.

How long is the sequencing queue?

We sequence on a first-come-first-served basis, and as a result the turnaround time for NGS varies throughout the year with demand. For up-to-date queue length information, check our twitter feed (also available on the right hand side of this website). Under average demand we expect a turnaround time of approximately 3-4 weeks for HiSeq, and 2 weeks for MiSeq.

If you have an unusually urgent sequencing request, please  and we can discuss giving your sample a higher priority status. We need to get a request fomr your group leader, and we'll do what we can to help.

How long is the library prep queue?

We make libraries on a first-come-first-served basis, abut we also try to batch samples together for efficiency. The turnaround time has been about 40 days from samples in to data out, but we do more RNA-seq and exomes than anything else. As a result the turnaround time for varies throughout the year with demand.

I know nothing about NGS: where do I start?

Why not read the Genomics core blog: "Help I really don't kow anything about NGS" written by Sarah.

How do I choose between RNA-seq and microarrays?

Why not read the Genomics core blog: "To seq or not to seq that is the DGE question" written by Michelle.

How do I choose between MiSeq, NextSeq and HiSeq?

We're busy wrting a blog post about this, for now get in touch by .

How do I sequence an exome?

Exome capture is generally performed using biotinylated oligo "baits" to capture and enrich exonic fragments from a whole genome sequencing library. We use Illumina's rapid exome capture kits as standard, it is possible to get other exome kits and custom capture kits from Illumina, Agilent, Nimblegen, and other providers

I didn’t use a Truseq kit for library preparation. Is that a problem?

It depends. As long as you used a library preparation kit or protocol which is designed for use on an Illumina sequencer, you should be fine. However, there are two important problems to look out for:

  • Do you need a custom primer? Read your protocol carefully to determine if it uses the standard Illumina primers, both for the insert and for the index read. Use these instructions if you need a custom primer
  • Are your index sequences already in our LIMS? Check our submission spreadsheet carefully to find out whether any of our known indexes use the same sequence as yours. If not, it is very important that you tell us about your indexes before you submit. Instructions if you need to add index information

How to check library QC/QT?

Why not read the Genomics core blog: "How do I know if my library is any good" written by Sarah.

Why does my data look bad?

We're busy wrting a blog post about this, for now get in touch by .

How long do you keep my NGS library?

We've never thrown one out yet! We'll keep libraries until we run out of space and then start getting rid of them. We ask you to submit only a portion of your libarary so you should always have a stock, and the genomics core should not be considered as a storage facility! Usually we've got your library and enough left for another run, but this depends on how much you gave us in the first place and whether we had to do any repeats.

LIMs FAQ:

How do I get a LabLink login?

Take a look at our submission guidelines page. If you are unsure do check with us as issues with submissions are likely to delay your project.

My sample sheet wont load?

This can be difficult to resolve without some more information from you, please take a scrrenshot or send us your error message by .

How long will you keep my data?

If you are in the building then data is archived and you should speak to Bioinformatics and IT. If you are outside the Institute then this is stated in the service agreement, and is currently 30 days on FTP.

What format will my results be in?

You will always receive FASTQ files, sometimes more! See this document which explains how we're doing things today. If it looks out of date then it probably is so get in touch directly by .