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Question: Database Of Known Chip-Seq Peaks
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gravatar for Bogdan Tanasa
5.2 years ago by
Bogdan Tanasa • 20
United States
Bogdan Tanasa • 20 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
chip-seq • 1.3k views
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modified 5.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 5.2 years ago by Bogdan Tanasa • 20
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gravatar for Jennifer Hillman Jackson
5.2 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
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 -- Jennifer Hillman-Jackson http://galaxyproject.org
ADD COMMENT • link written 5.2 years ago by Jennifer Hillman Jackson ♦ 25k
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