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GeneProf Manual

Manual as PDF

Florian Halbritter, 27-Nov-2012

Table of Contents

Chapter: Introduction

Chapter: Concepts Explained

Chapter: Tutorials

Chapter: Modules

Click here to expand this category.
  • General Tools
  • Sequence Data Operations
  • Genomic Region Operations
  • Feature Data Operations
  • Parsers
  • Alignment
  • Reference Set Manipulation
  • Transcriptomics
  • ChIP-seq
  • Post-Processing
  • Summary Statistics
  • Meta

    • Chapter: Pages

    Chapter: Advanced Topics

    Chapter: Frequently Asked Questions (FAQ)

    Frequently Asked Questions (FAQ)

    How do I cite GeneProf?
    If you publish your research benefitting from GeneProf-assisted analysis or data, please cite the original GeneProf paper:
    Halbritter F, Vaidya HJ, Tomlinson SR. GeneProf: analysis of high-throughput sequencing experiments. Nature Methods 9, 7-8 (2012).
    How do I go about publishing my GeneProf analyses in papers?
    1. To provide pre-publication access to researchers, you can enable password-based sharing of your experiment from the experiment main page by clicking the 'Share your experiment with other users' link and activating the option on the next page. GeneProf will email a password to you that you may pass on to the reviewers (or the editor).
    2. In the data/methods section of the paper, please cite GeneProf [1] and quote the accession number(s) of relevant GeneProf experiments (something of the form 'gpXP_xxxxxx'). Ideally, provide a direct link to the experiment using the URL shown as 'Permalink' on the experiment main page.
    3. If allowed by the journal, attach a copy of the experiment PDF report to the supplementary materials for the paper.
    4. After your paper has been accepted (yay!), make the experiment public.
    Can I use GeneProf to analyse data from my favourite organism?
    We support a range of well-studied model organisms by default (see Section 'Natively Supported Organisms'). Alternatively, you can define your own reference datasets and use those in your analyses (see Tutorial 'Creating a Custom Reference Set').
    Does GeneProf support transcriptome / genome assembly?
    No, not yet, sorry. We'd like to add support for de-novo transcriptome assembly in one of the future releases, but this might yet be some time. If you'd like to express your support for the implementation of this feature, have suggestions for appropriate tools and methods or any other comments, subscribe and comment on this feature request.

    Bibliography

    [1] Halbritter, F and Vaidya, HJ and Tomlinson, SR. GeneProf: analysis of high-throughput sequencing experiments. Nat. Methods (2011). PMID: 22205509.