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
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
--
Jennifer Hillman-Jackson
http://galaxyproject.org
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
