CTSC Biomedical Informatics Core to Offer CTSC Partners Free Training and Access to NYoSh Data Analysis Workbench for High-Throughput Sequencing Analysis

The biomedical informatics core of the CTSC is starting to offer the NYoSh Data Analysis Workbench to analyze high-throughput sequencing (HTS) data. This Data Analysis Workbench is being developed to facilitate data analysis for biomedical scientists with minimal computational skills. The software is fully functional, open-source, and provided free of charge.

The software runs as a desktop application on Mac computers. Most data analyses require access to a Linux compute cluster running Sun Grid Engine (provided by the CTSC for institutional users). Training and assistance in the use of the software is offered to investigators who hold an appointment in one of our CTSC institutions (i.e., Weill Cornell, MSKCC, HSS, and Hunter College).

The analysis workbench currently supports all the analysis plugins developed for GobyWeb, including for the following assays:

  • RNA-Seq
  • smallRNA-Seq
  • Methyl-Seq,
  • Reduced Representation Bisulfite Sequencing (RRBS & ERRBS)
  • DNA-Seq

The software also supports:

  • Trio Analysis
  • Somatic Variation Analyses
  • Detection of pathogens in HTS datasets
  • Detection of differential splicing across groups
  • Full compatibility with the Integrative Genomics Viewer for easy visualization of gene expression, DNA methylation and genotype processed data.

See http://workbench.campagnelab.org for more details and tutorials. Note that we continue to offer GobyWeb for investigators who need to manage large quantities of sequencing data and prefer a fully turn-key solution. We have developed the NYoSh Data Analysis Workbench to provide more flexibility during data analysis than is possible to offer with a web application.

Training Sessions:
Users interested in learning how to use the software are encouraged to attend one of the monthly two-hour training sessions. Training sessions are held on Tuesdays at 10:30 AM. Training sessions are limited to participants and pre-registration is required.

Please use the registration form to reserve a seat. The first training session will be held Nov 25th 2014.

Participants will be shown how to use the software to analyze RNA-Seq data. There is no charge for training and you are encouraged to attend the training session to determine if the NYoSh Analysis Workbench can help with your projects.

Pre-requisites:
No programming or UNIX skills are required and the software will run on Mac OS 10.7+ ITS-tagged laptops (the ITS tag is needed during training to make sure all trainees can access the CTSC compute grid using the ITS wireless).

This software is provided by the Biomedical Informatics Core of the Clinical and Translational Science Center and by the Campagne laboratory.

Please contact Dr. Fabien Campagne if you have any questions or comments at 646-962-5613.

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