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Question: De-Novo Motif Analysis
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gravatar for Christopher Futtner
7.8 years ago by
Christopher Futtner • 20
Christopher Futtner • 20 wrote:
Two questions - 1. When I call peaks with MACS on Galaxy I get different results than if I run MACS on my machine via command line. I'm using default parameters in both instances. 2. Are there any tools in galaxy for doing de-novo motif analysis of the peaks that I have called. If not can anyone suggest their favorite programs for doing so? I prefer a web interface but can fumble my way around using command line. Thanks, Chris Christopher Futtner Duke University, Onaitis Lab 919-684-1183 106 Research Dr. MSRB II, rm. 2045 Bay 11 Durham, NC. 27710
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modified 7.8 years ago by vasu punj • 360 • written 7.8 years ago by Christopher Futtner • 20
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gravatar for vasu punj
7.8 years ago by
vasu punj • 360
vasu punj • 360 wrote:
If it is ChIP-motif you may like to consider http://motif.bmi.ohio- state.edu/ChIPMotifs/ There are several others but this is my favorite.   Vasu Punj Subject: [galaxy-user] de-novo motif analysis To: galaxy-user@bx.psu.edu Date: Friday, February 25, 2011, 2:13 PM Two questions - 1. When I call peaks with MACS on Galaxy I get different results than if I run MACS on my machine via command line. I'm using default parameters in both instances. 2. Are there any tools in galaxy for doing de-novo motif analysis of the peaks that I have called. If not can anyone suggest their favorite programs for doing so? I prefer a web interface but can fumble my way around using command line. Thanks, Chris Christopher Futtner Duke University, Onaitis Lab 919-684-1183 106 Research Dr. MSRB II, rm. 2045 Bay 11 Durham, NC. 27710 _______________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. 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/
ADD COMMENT • link written 7.8 years ago by vasu punj • 360
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