Deep Sequencing Resources and User Information

You will need an account on the High Performance Computing Cluster.
To get an account, contact the UMass Med Help Desk at 856 - 8643
or email them at
 
UMWHelpdesk@UMassMed.edu   
There is a Guide for UNIX at
http://biotools.umassmed.edu
The WIKI for the HPCC is at http://wiki.umassmed.edu/rc/wiki

Our current data "delivery" system
(note this changes as resources improve/upgrade, so stay tuned): 
~ Your lab or working group will have a directory at
    /nearline/deepseq/
~  You will get an email notification when your data files are ready
~  If you require anything besides the Bustard output (includes fastq file)
    you must let us know at the time you submit your sample
~  Data files will be deleted after 10 days, please
    backup/copy/archive your data in your own workspace.

Protocols and sample submission information are available on the SERVICES page.
Please click the SERVICES link in the left nav for more information.

Technical Bulletins, analytical tools, and BioInformatics information are being collected and posted on the DeepSeq_Data Page.

Publications and information about deep sequencing (MPSS) can be found on the Publications page at Illumina ( link ). We recommend starting with the review
by 
DR Bentley, "Whole-genome re-sequencing". 

The NIH Gene Expression Omnibus accepts Next Generation or Deep Sequencing data. Information about data submission and links to the tools at GEO may be found on the GEO Page. 

Many UMass Bioinformatics resources can be found at http://biotools.umassmed.edu

We are establishing a library of reference genomes and analysis tools, we welcome requests
and suggestions. 
 
Nemo@umassmed.edu

 ~  Nemo and Crew

Click here to meet NEMO !