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Frequently Asked Questions
1. How much does sequencing cost?
Cost can vary depending upon how much sequencing you need. We suggest you visit Illumina's support pages for a "coverage calculator", their Sequencing method explorer and custom protocol selector. The NextSeq500 produces up to 120Gbp of sequence data from up to 400,000,000 reads.
2. How do I submit a sample for sequencing?
Please contact us and arrange for your samples to be brought to the Genomics center at a mutually acceptable time.
3. Can I multiplex samples?
Yes and we expect lots of multiplex samples with indexes. Please remember that multiplexed samples should all use the same (single or dual) number of indexes, and that they should all have approximately the same total length. We can multiplex, and then demultiplex samples with either 6bp, 8bp or 12bp indexes. We support single or dual indexed libraries. It is important that we know exactly which index(es) you use for each sample.
4. What is cross-talk?
Cross-talk is when sequencing errors cause reads to be placed in the wrong index group after demultiplexing. The NextSeq has the lowest measured cross-talk of all Illumina instruments.
5. How much of a sample do you need?
It depends. Determine which library kit, and sequencing kit you need. We prefer at least 300ng in 30ul of water. TruSeq no-PCR kits require at least 2 micrograms of sample. Nextera kits can use as little as 50 nanograms or even 1 nanogram of sample. Use Illumina's support pages to help you decide what is best for you, but generally starting with larger amounts gives better data.
6. How can I tell if my sample is good enough to sequence?
We suggest you submit gel-images of your samples, then pay for the Genomics center
to do quality-control on your samples using fluorometric determinations ($4 to $10),
Bioanalyzer analyses ($4-$60)*, and qPCR ($20-$40). If you do your sequencing with
us, these charges can be waived unless they must be repeated.
*There are multiple options for Bioanalyzer analyses before and after library production.
7. What happens if my samples are good?
They will be entered into the sequencing queue starting at the library prep stage, or the sequencing stage (if you have prepared your own libraries). An Invoice for all charges will be produced which is due at the conclusion of sequencing.
8. Where will my data be stored?
You should keep a local copy of your sequencing data. During sequencing, data are streamed to the OSU-TIGER cloud (part of the Cowboy supercomputer), where it is demultiplexed and cleaned as needed. We then send you a direct link for downloading.
9. How long will the Genomics Center store my data?
We will store your data locally on the cloud for one month. After that it will be moved to archival long-term storage at the Oklahoma Petastore. If you wish to retrieve your data from the Petastore we can do it for a $35 charge. If you do not wish for your data to be archived, TELL US, it will simply be deleted from local storage.
10. Will the Genomics Center analyze my data for me?
Some analyses can be done at the Genomics Center under collaborative arrangements, or using a fee-for-service of $35 per hour. Unfortunately, our availability is sporadic, and can be limited. Alternatively, analyses can be done by the Bioinformatics specialist in the HPCC. To learn how to analyze your data, we suggest attending bioinformatics workshops/classes, software carpentry workshops, or taking online bioinformatics modules as they are developed.
11. How long will it take to get my sequencing data?
The longest run on the instrument is 28 hours. The longest library preps take 2.5 days. If you want your data rapidly, assemble enough samples to use an entire sequencing run. You may want to mix samples with another researcher and split the costs. At peak usage, we run the instrument 2-3 times a week. Turnaround times will likely be longer as we build a clientèle and queue. For concerns please contact us.
12. Can you perform 16S/18S RNA analyses?
Not really, and it depends. Most conventional 16S/18S analysis use longer sequences than we can produce, however, there are shorter 16S/18S regions that are often used, or multiple regions can be used. Because of the complexity of these projects it is best if you contact the Genomics center before starting your experiment.
I'm confused about...
Contact the Genomics Center and arrange for a meeting with Dr. Hoyt or Dr. Hwang.