Hello Bogdan,

The ENCODE project is a very large collection of expression data that includes ChIP-seq. You can find this in the UCSC Genome Browser. There is an ENCODE portal and a google group if you have questions about usage or content. The datasets can be imported into Galaxy for further analysis. The UCSC Genome Browser is at: http://genome.ucsc.edu


A quick google on "ChIP-seq data" will bring up alternate sources, such as the NCBI GEO collection. Searching NCBI's PubMed will also pick up publications, which can help orient you to current projects, data collections, and methodologies.

For analysis, common tools for peak calling can be found on the public Main Galaxy instance in the tool group:
NGS: Peak Calling

Example analysis using these Galaxy wrapped tools (on Main or in the Tool Shed, see below) can be found here:
https://main.g2.bx.psu.edu/u/james/p/exercise-chip-seq
https://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012 (Protocol 3)
http://wiki.galaxyproject.org/Learn#Other_Tutorials

Other public Galaxy servers contain additional analysis tools & tutorials, you can review the options here:
http://wiki.galaxyproject.org/PublicGalaxyServers

Additional tools for analysis of interest (if you have a specific publication in mind you are wanting to follow) may have tools wrapped and available in the Tool Shed. These are for use in a local, cloud, or slipstream Galaxy. The links to get started are on these wikis:
http://wiki.galaxyproject.org/BigPicture/Choices
http://toolshed.g2.bx.psu.edu/
http://wiki.galaxyproject.org/Tool%20Shed See 4.4 for Installation, etc.
http://vimeo.com/channels/581769 See Channel: Galaxy ToolShed


Hopefully one or more of these options will work out for you!

Jen
Galaxy team

On 9/26/13 1:14 PM, Bogdan Tanasa wrote:
Dear all,

please could you recommend any resource/collection/database of known ChIP-seq tracks that also include a significance analysis tool ?

thanks,

Bogdan


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The Galaxy User list should be used for the discussion of
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