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Bioinformatics

The Bioinformatics Shared Resource (BSR) provides essential services and technical support for Next Gen Sequencing (NGS) analysis. From providing advice at the planning stages of data-intensive experiments to developing customized software tools for analyzing data, the BSR works closely with Cancer Center members to support CSHL research projects. We also encourage Cancer Center members to learn the basic techniques of bioinformatic analysis. The BSR is happy to guide Cancer Center members in using web-based interfaces to access sophisticated computational tools, enabling CSHL researchers to do much of the analysis on their own. For more information see below, or contact the Resource Director, Alex Dobin, Ph.D.

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Shared Resource Staff

Resource Head

Peter Koo, Ph.D.
koo@cshl.edu

Director

Rad Utama, Ph.D.
utama@cshl.edu

Custom Software Development
The Bioinformatics Shared Resource provides custom software consulting and data mining services for a variety of specialized scientific applications. Whether your experiment is still in the planning stages or data generation has been completed, our staff can provide advice, assistance, and analysis.

Custom Experimental Design and Analysis
Because of their specialized experience in analyzing NGS data, the BSR staff can provide up-front guidance on experimental design and choice of platforms best suited to the goals of Cancer Center research. Interactions with researchers range from short-term data mining consultations to long-term customized database development spanning several months.

Shared BioComputing Software
The BSR maintains a selected list of web resources (CSHL internal link) for common bioinformatics tasks. For more computationally intensive procedures, the BSR maintains a private Galaxy server (CSHL internal link) that provides a user-friendly interface for sophisticated data analysis tools running on the High Performance Computing Cluster.

The BSR runs periodic campus-wide training courses in basic bioinformatics techniques and resources both within and outside the CSHL campus. Contact the BSR for assistance with local software installations or for individual training sessions.

Here are some links to useful analysis tools. For further assistance contact the BSR.

  • RNA-seq analysis
    • STAR to align to the genome/transcriptome
    • HTSeq for gene quantification
    • R-based methods, such as edgeR and DESeq for differential analysis.
  • ChIP-seq analysis
    • Mapping transcription factor binding sites with MACS
    • Mapping chromatin binding factors or marked histones with SICER
  • Variant Calling
  • NGS Questions and Answers
    • Chances are someone else has run into the similar issues with NGS analysis. Try browsing or posting on the seqanswers forum.
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Cold Spring Harbor Laboratory is an NCI-designated Cancer Center. As a basic research institution, CSHL does not treat patients. Information about individual cancers is available at the NCI CancerNet. Questions about CSHL’s cancer research program should be directed to our Communications Department.