How Long is THE QUEUE ???
This FAQ (frequently asked question) is so popular that it deserves its own page!
We are working on a real-time, interactive status system, but until that can be implemented, here is information which we hope will be helpful.
The blue status box shown here is the prototype.
Until it is active you may email us at DeepSequencingCoreLabs@umassmed.edu
and ask where your sample(s) is now. Please include the name of your PI and the name of the sample(s).
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 BioAnalyzer service for a small fee (that is listed on the website at www.umassmed.edu/MBCL).
The initial QC is usually a BioAnalyzer trace, possibly with a Q-PCR or Pico-green assay depending on the platform and type of sample you submitted. This procedure usually takes 2-3 BUSINESS Days. Once the sample passes QC to our satisfaction, we send you the BA traces and 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 time from QC-pass to the start of imaging depends on several factors, including instrument availability, reagent status (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 as we
do single read 36's. Conversely, if you turn in some SR36 samples, you might wait while all the other SR36'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 GAIIs or the HiSeqs, please note that we need 7 samples to start up a run (lane 8 is a requisite control). At the request of our users, we will begin including information on this part of the queue when we send the QC information.
IF YOU ARE IN A HURRY, YOU MIGHT CONSIDER SELECTING SEVERAL
CONFIGURATIONS ON YOUR TICKET AND WRITING ON THE TICKET.
"USE FIRST AVAILABLE"
For example if your PE36 could be analyzed as a PE50 instead or vice versa, note
that on the ticket and you'll get onto whichever type of run that goes next.
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.
If you have a large number of samples coming in, please 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.
The next part of the "queue" is not really a queue ... it's a "wait".
The instruments need time to perform the chemistry and image each cycle. If your read is longer this will take more time. If you are doing a paired read, add 1 more Business Day for the building of the reverse orientation. If you are doing a long read on the HiSeq, that's a lot more data to transfer than the data from a short read on the GAII so the data transfer takes longer, ... and so does the pipeline which does the basecalling. Pipeline times vary depending on the activity on the HPCC and other computer phenomena.
We can't give you any performance info until the pipeline is finished.
If you need to know where a sample is in this process, please email us at
DeepSequencingCoreLabs@umassmed.edu and give us 1 Business day to respond.
We can't make it go faster but we can let you know where things are.