Frequently Asked Questions
FAQ – General
Diving into sequencing for a new project and placing a sequencing order can be overwhelming. We collected some of the most commonly asked questions here (in addition to the tips and recommendations on our individual service pages) to help ease some of that pressure.
To help you navigate, the “expand all” button will open all answers to allow in-browser search functionality. If you have a question not covered here, please do not hesitate to contact us at info@seqcenter.com!
We offer DNA, RNA, and dedicated flowcell short read sequencing on our Illumina machines, as well as long read sequencing on Oxford Nanopore and PacBio machines. For additional information, please visit our pipeline overview and specific service pages using the “Services” navigation menu.
We unfortunately do not offer Sanger sequencing services.
Our library preparation pipelines are very robust and accommodate a wide range of sample qualities. As such, we will attempt library preparation for all samples submitted as they are.
We ask our customers to evaluate the quality and quantity of their samples before sending and ensure they meet our submission standards as well as requirements of their project. In some instances, we are able to accommodate samples submitted below requirements, but custom arrangements must be made in advance. Please refer to each specific pipeline’s service page for recommendations for submissions, our submission FAQ page for information about samples that do not meet our requirements, and our policies page for more information on our failed sample policies.
The window starts once we receive all necessary parts of the order, including all samples, a payment method, and any information needed to process the samples or analyses. If any additional information is needed or an order is modified, the timeframe will be reset.
Unfortunately, custom services and orders are not covered in this two-week turnaround time. We will still target this two-week window, but the timeframe for custom work cannot be guaranteed.
All of our standard services are guaranteed within a two-week turnaround window, which is set by the date upon which we receive all pieces of an order. This includes all samples, a payment method, and any additional files or information needed to process the order and analyses. Specific data outputs are unique to each of our services and can be found in the individual service’s page using the “Services” drop down arrow from our home page.
We unfortunately cannot guarantee results sooner than two weeks, though we make our best efforts to deliver all orders as quickly as possible.
Custom projects and quotes are not covered by the two-week guarantee, but every effort is made to stay as close to the two-week window as possible.
Data is uploaded to Box.com and then shared with the customer in two ways. An editor invite is sent out via Box.com to the primary email address of the order, giving the customer access and permission to share and manipulate the data. An additional link to the data is sent by email to the same address; this link provides access without a Box.com account. We highly recommend that customers download local copies of all data. Please see our policies page for more information on our data retention window.
We are able to accommodate alternative distribution methods, though these may be delivered outside of the two-week window and may require additional setup. Please contact us if you would prefer an alternative method.
Box.com is a cloud-based data storage service that supports free-to-use accounts tied to an email address. Data can be downloaded with a free account. (SeqCenter hosts the data. Please see our policies page for more details about our data retention timelines.) Some academic institutions have existing contracts with Box.com, which may allow for larger or faster transfers. Box also provides a CLI to facilitate bulk data transfers. More information can be found on their CLI documentation page and GitHub page.
The exact output varies by service. Please see the individual service pages for full file lists.
In general, all sequencing orders will include at least raw reads in fastq format, a methods document, and a summary of some overall sequencing statistics for each sample. The .fastq files are raw, unassembled reads with adapter sequences trimmed.
Quote generation (and order processing) for our standard services is handled directly through our website. To obtain a quote, you only need to complete through Step 2, after which an email with a pdf quote is sent to the address entered. You are more than welcome to create as many quotes as you would like, and there is no obligation to cancel a quote. To return to a quote at a later date, you can either use the hyperlink provided in the quote email or the “Access a Quote” tab from our homepage.
For service requests outside of our standard packages, please contact us for a custom quote.
You can proceed straight from quote generation to order submission directly through our website. If you already generated a quote, you can return to an existing quote by using either the hyperlink in the quote email or the “Access a Quote” tab from our homepage.
To complete checkout, you are required to complete Step 3 (Sample Details) and Step 4 (Submit Payment). In Step 3, you are prompted to input sample names, concentrations, and select which samples are receiving analysis, if applicable. In Step 4, payment information (credit card or purchase order) is added.
Only custom quotes/orders need to be placed with a SeqCenter representative.
For any analysis requiring a reference, provide any one of the following:
- Assembly file (ending in ONLY .gb, .gbff, .gbk, .tar, .fasta, .fa, .fna).
- Annotated files (.gb, .gbk, .gbff) files are required for RNA analysis and recommended for variant calling, as the output will include gene information.
- .fna and often .fasta files contain nucleotide information only.
- NCBI Accession Number as text in the Comments box. (Accession numbers start with GCA, GCF, NC, etc.)
- Please ensure that the number provided aligns to the annotation set you want.
- GenBank and RefSeq annotations will differ in locus tag and can differ in number of predicted orfs or functional annotations. The customer must choose one or the other.
- Nanopore Combo or Assembly sample from current or previous order, including the order number, referenced as text in the Comments box.
Before the samples arrive at our facility, we recommend keeping a close eye on the courier tracking for your shipment in case of any unexpected shipping delays. Once the package arrives at our facility, our team carefully reviews the samples and corresponding order.
After an order is reviewed, you will receive an automated email from us notifying you that your samples arrived. If the team has any questions or comments, these are listed in the email. There may be a small delay between when the courier marks a package as delivered and when you receive your notification, and occasionally these notifications are flagged as spam. Please check your spam if you do not see an email.
Unfortunately, at this time, most adjustments to existing quotes and orders are not possible through our website.
If you would like to add samples or analyses to your quote order, please place a new, separate order for the additional services (or a replacement order).
If the changes only apply to sample names and sample concentrations, we are able to make the corresponding changes internally. Please reply to either your order confirmation email or the email that shared the quote with details of the changes.
If you would like to decrease the number of samples on your order, please make note of the decrease during your submission. We will remove the samples that are no longer required from the order during the billing process. You are only billed for the samples that were sequenced.
Unfortunately, we do not offer expedited service. Our guaranteed turnaround time of two weeks is an industry best and is representative of many other sequencing service providers’ expedited service times.
We are happy to try to accommodate high priority orders as we can, free of charge, but we cannot guarantee that we will meet a specific deadline that falls before the end of the standard two-week window.
We are happy to help get you started with your analysis, though we cannot provide interpretations or support for third party programs. If your order included analysis, the analysis methods document includes additional information and resources which can provide a great launching point, as well.
If you are looking for a bioinformatic program with a graphical interface, Galaxy and Geneious are two popular and powerful tools, with plenty of documentation. KBase is also a fantastic cloud-based platform that hosts many common command-line packages in point-and-click format along with a large plethora of premade pipelines and tutorials.
Additionally, we offer several standard add-on analysis packages and would love to discuss what custom analysis services we are able to provide for your specific project, if the standard services do not meet your needs.
Of course, if there are any issues with your data, please contact us so that we can begin investigating immediately.
Our facilities will be closed for specific holidays, and we will be unable to accept packages during those days. Additionally, the closures will offset the two-week deadline for orders for which the turnaround window includes the dates listed below. (Please see our policies page for more information on our two-week turnaround window.)
2024 Closures
- Monday, Jan 15, 2024 (Martin Luther King Jr. Day)
- Monday, May 27, 2024 (US Memorial Day)
- Thursday, July 4, 2024 (US Independence Day)
- Monday, Sept 2, 2024 (US Labor Day)
- Thursday, Nov 28, 2024 through Sunday, Dec 1, 2024 (Thanksgiving)
- Saturday, Dec 21, 2024 through Wednesday, Jan 1, 2025 (Winter Break)
We only ask that the methods section states that the specific services ordered were performed by SeqCenter in Pittsburgh, PA, with service specifics being derived from the methods documents provided with each order.
