This FAQ (frequently asked question) is so popular that it deserves its own page!
At this time, if you need to know where a sample is in this process, the only way to find out is to please email us at DeepSequencingCoreLabs@umassmed.edu and give us 1 business day to respond.
We can't give you any performance info until the pipeline is finished.
The queue for a short-insert, well made library is usually a couple of weeks (and could be one week for MiSeq runs). The queue for a library with long inserts which is poorly made or which has a wide range of insert sizes can be over a month, especially if there needs to be effort spent on getting it into a useable condition. We QC using Fragment Analyzer evaluation and if there are concerns at this point we contact you immediately. The sooner you can respond and help with any adjustments, the quicker the sample can move to the next step.
Build a good, tightly-sized, clean library and share information with us about any residual linkers or primer sequences, barcodes, adapters, polyA stretches, even the results of your test sequencing of the Topo clones can be helpful.
Other than that, we are a first-come, first-serve facility. We cannot prioritize your sample ahead of others.
If a user needs to analyze an inordinate number of samples which would set back everyone else, we will work with them to create a schedule that does not negatively impact the other users. (So if you have 120 samples, email us well in advance please. This will also give us as much notice as possible so we can have the reagents in stock and will be ready to get them moving as soon as they arrive).
IF YOU ARE IN A HURRY, YOU MIGHT CONSIDER SELECTING SEVERAL CONFIGURATIONS ON YOUR TICKET AND CHECKING ON THE TICKET "USE FIRST AVAILABLE"
For example if your SR50 could be analyzed as a SR100 instead or vice versa, note that on the ticket and you'll get onto whichever type of run that goes next. (In this case, you will be invoiced for whichever run type is used.)
IF YOU ARE IN A BIG BIG HURRY ....
Since the reason for the queue and the wait is to fill the flow cells and keep costs down, you could fill the flow cell. If you are willing to purchase the unused lanes and fill them with archived samples of yours which might benefit from another run or even run the new sample in several lanes for additional depth, then let us know. We will work with you to get things going as fast as we can.
The first part of the queue includes sample submission, login, and intial QC.
When you submit a sample, it is with the understanding that you are ready to go and have done your validation sequencing and workup. Submitting several samples "just to see how they look" is not good practice. You may send them to the Fragment Analyzer service or any other QC you choose ahead of submission. The initial QC is usually a Fragment Analyzer trace, possibly with a Q-PCR or Qubit assay depending on the platform and type of sample you submitted. This procedure usually takes 1-2 BUSINESS days. Once the sample passes QC to our satisfaction, we move to the next step. If it does not pass, you will receive a note with a copy of the trace data. You can then work with us to further process the sample or you can ask for it to be run as-is but without any assurance of quality or output.
The next part of the queue is the time from QC-pass to the start of sequencing.
The wait depends on several factors, including instrument availability, reagent status (if backordered), but most critical is the number of other samples waiting for the same type of run. If you turned in 1 single read 100 sample you might wait longer since we don't get as many of those. Conversely, if you turn in some PE50 samples, you might wait while all the other PE50's ahead of you are run. Samples are run on a first-in first-on basis. Lots of samples ahead of you means a longer wait time. There are 8 lanes on an Illumina flow cell. If you are waiting for the HiSeqs, please note that we need 7 samples to start up a run (lane 8 is a requisite control).
The next part of the "queue" is the time to perform the cluster generation, chemistry, and image each cycle.
This varies by platform (HiSeq vs MiSeq). If your read is longer it will take more time. If you are doing a paired read, add 1 more business day for the building of the reverse orientation.
The final stages are the pipeline which does the basecalling, and data transfer.
Pipeline and transfer times vary depending on run length, the activity on HPCC (the High Performance Computing Cluster), and other computer phenomena. Some of these factors (such as HPCC down-time or data transfer using other methods like portable hard drives), are beyond our control.