Deep Sequencing Core Facility

  The Pacific BioSciences RS Instrument is here and running samples !
  The Website for the new PacBio Enterprise is under construction ... http://www.umassmed.edu/PacBio.aspx

Please use this Sequencing Sample Ticket (Feb 2013) for all DeepSeq samples, including HiSeq. For a pricing list or other HiSeq questions, please email us.

The UMass MBCL is now building genomic DNA libraries for HiSeq analysis.
Please email us to inquire about scheduling, etc.!

There is an updated list of sequences for Illumina library construction. If you are UMass investigator and wish to obtain a copy, please send an email to NEMO@umassmed.edu and request "the new oligo list".

"How Long is THE QUEUE" FAQ is here

A list of frequently asked questions and some answers are here
Puzzled about Multiplexing and Barcoding? Click Here.

 

 

 

 

 

NOTE: It is VERY IMPORTANT that we receive the correct information about the primers and adapters used to build your library! Not all library types will run on the HiSeq instruments or can be read in both directions. If you are using the Illumina internal barcodes in the TruSeq adapaters, you must add a multiplex read step to detect your barcodes. There is more information in the FAQ.

IF THERE IS A PROBLEM WITH YOUR RUN OR QUESTIONS ABOUT YOUR DATA, please let us know as soon as possible. The run metrics and machine files cannot be held for long since they are large, the sooner we know there is a problem, the more likely we'll be able to help easily.  Also, please note that in order to help sort out a problem we may ask alot of questions and details about your sample and your analysis methods. This information is required inorder for us to engage the tech support systems provided by our vendors. Please note that if the control lane on the run failed in any way, the entire flow cell is rerun. If your data is delivered to you, then the controls all passed spec. which means that the instrument functioned properly and the reagents and chemistry worked. That leaves us with investigating other issues including sample design, base balance, sizing, indexing, degraded DNA, as well as computational and analysis issues with the pipeline, etc. We'll do whatever we can to get things working, but the more information we have, the better. We are working on a trouble-shooting guide for libraries, it is under construction and is starting to come together here.

We are building a new resources section. If you have a protocol or publication that you found useful, please share. If you have a request for something you think would be beneficial, please let us know, email us at DeepSequencingCoreLabs@umassmed.edu

If you would like to consult with an applications specialist, please email us to get on the schedule.

Link to BioTools for Next Gen Sequencing Documents click here
Information about NextGen BioInformatics Tools on HPCC click here

For a letter of support for your grant, click here

New Tool for Data Quality Score Viewing FASTQC

Payment Policy:  Processing and analyzing a sample requires time and reagents. Payment for these services is the responsibility of the user submitting the sample. In the event of a reagent or equipment failure, the samples will be rerun at the next possible opportunity at no additional charge.

WEATHER ALERT ~ ~ ~ In case of extreme and/or inconvenient weather, the machines will still be running but we may not be here for sample login. Please email us to arrange drop off if the weather is questionable. 

NEMO@umassmed.edu