SGT Frequently Asked Questions

Ordering & Submission

Most next generation sequencing projects require special consideration. We recommend contacting us before initiating a project with SGT. Choosing the correct DNA and RNA sequencing service for your samples depends on the organism, total nucleic acids available for input, and project goals. Please see the Resources page for information and tutorials on next generation sequencing.

f you know which service you would like, you can use DUGSIM to estimate the cost of your project. Using the “Estimate Cost” button you can select the services that you require and submit the request for a quote. See our Ordering page for more details. If you are unfamiliar with the different technologies and desire a consultation, contact us.

We are a cost-recovery shared resource and do not make a profit on our services per Duke policy. Our price includes our facility fee for our services and the cost of consumables. Per Duke policy, there are no discounts on services.

All requests must be made using our laboratory information management system DUGSIM. Visit our Ordering page for more information on how to use DUGSIM.

No samples may be accepted until you have placed an order in DUGSIM. Once an order is placed, you may submit samples on campus, directly to us on campus, or mail them to us. Please see Sample Submission Guidelines for more information.

Note: We will return samples if not in the proper plating format. Our requirements ensure that we can perform the best experiments both effectively and efficiently. If by any chance you cannot replate your samples, we will charge a $2/sample preparation service, and do not take responsibility for mislabeled or lost samples.

After you have received your order number, samples should be shipped on blue ice or dry ice. Please include a printout of your order with your shipment. Detailed information about how and where to ship your samples can be found under Ordering.

We will run QC on your samples using a Qubit measurement followed by a Bioanalyzer or Tapestation evaluation. If your samples look questionable or disagree with the information you supplied, we will contact you before proceeding. We only send QC results if there is a problem with your samples or if you have specifically requested them before we proceed with your order. 

Yes, we can QC more samples than you sequence. However, you must have a sequencing order and submit ample volume of sample for us to proceed with the order (6 ul for QC). While we no longer offer QC only services, the Microbiome Core Facility does.  

Orders enter our queue upon receipt of samples and no earlier. Average queue times are posted on our Services page. The length of time will depend on the type of run, whether we are preparing your libraries and our current volume of requests. It may also be influenced by kit availability and any unforeseen technical issues. We also are not able to predict queue times on lane purchases.

Be assured that we do our best to generate your data as soon as possible.

Yes, but please indicate in the comment box of your quote/order that you want your samples back. You can either add a comment to that effect in the comment box of your quote/order or email us at Unless noted by the client, all samples are discarded three months after data delivery.

Custom sequencing & Client prepared libraries

We do not guarantee the sequencing results for any custom sequencing or client prepared libraries. Please familiarize yourself with our instruments and provide as much information as possible (loading concentration, % PhiX, samples to be pooled together on a lane, etc.) to increase the success of your sequencing run. We will load customer prepared libraries according to the directions provided. If a run fails due to missing or erroneous directions including but not limited to incorrect library or loading concentrations, mislabeled barcodes, incorrect sequencing protocol, it is the responsibility of the client to pay for the failed sequencing run and any subsequent sequencing runs.

If you have any questions before submitting your custom sequencing or client prepared libraries, please contact us.

You may submit your own library or pools of libraries. Requirements will vary depending on the sequencer you plan on using and can be found on our Sample Requirements page

Additionally, any clients requesting custom sequencing runs (e.g. custom primers, custom sequencing protocols for 10x, etc.) must purchase a full flow cell.

We do not guarantee the sequencing results for any customer prepared libraries or customer primers. 

Yes, please familiarize yourself with our instruments to ensure your primers are correctly designed.

We do not guarantee the sequencing results for any customer prepared libraries or custom sequencing runs, including those with custom primers. 

While certain library preparations can consistently produce different fragment sizes (e.g. ATAC-seq), it will be very difficult to accurately calculate the molarity of your sample. If we can’t accurately determine the correct molarity of your library, it can lead to under or overloading of the flow cell (i.e. lower reads produced from a sequencing run). You will be asked to decide which fragment size you want to choose for the calculation, or if you want to proceed. 

As is the case with any customer prepared libraries, we do not guarantee the sequencing results.

We do not recommend mixing different library types to sequence together in the same pool. Different library preps, particularly when their insert sizes are different, can interfere with the sequencing efficiency of either library. However, we understand that it may be more cost-effective to pool different library preps together. We have recommendations to increase chances of a successful run, but do not guarantee the sequencing results. Please reach out to us if you have questions.

Data Delivery & Data Processing

For most sequencing runs, we will demultiplex your data and send you FASTQ files.

Yes! Data processing is $97/hour, and we provide Mapping and Basic QC, RNA-Seq processing, variant calling, and peak calling. Contact us for more information.

We can demultiplex 10x Genomics data. However, due to our current bandwidth, it will add two weeks until delivery time.

Data will be uploaded to an sftp server. Login and password to access the data will be sent by email once the data has been uploaded.

We do not have enough storage capacity to keep your data indefinitely on our server, so data is removed after one month from our sftp server. 

If your data was delivered using sftp, you can simply forward the email containing the login and password to your collaborators.

Most sequencing runs performed today are paired-end. This means you have a file from both ends of the insert (read 1 or R1 and read 2 or R2)

If your order was run on more than one lane, each lane will produce a separate sequencing file also (L001 – L004).

Miscellaneous Questions

Yes, email or schedule a consultation with us, and we would be happy to discuss your project.

For all publications that include data generated in the Sequencing and Genomic Technologies Shared Resource, we kindly request that you acknowledge this support:

We thank the Duke University School of Medicine for the use of the Sequencing and Genomic Technologies Shared Resource, which provided _________ service.

Invoices are generated after the sequencing results have been released.

Duke clients must supply a fund code before an order is generated. Non-Duke clients must provide a signed PO before an order number will be issued. Payments may be made by check. We do not accept credit cards or wire transfers.