Workflow Designer Documentation v. 1.15.0
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  • ChIP-seq Analysis with Cistrome Tools

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Note that it is originally based on the General ChIP-seq pipeline from the public Cistrome installation on the Galaxy workflow platform.

 

Tip
titleHow to Use This Sample

If you haven't used the workflow samples in UGENE before, look at the "How to Use Sample Workflows" section of the documentation.

Select Samples tab on the Workflow Designer Palette and double-click on the ChIP-seq analysis with Cistrome tools sample. The following wizard appears:

 

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  <img src="/wiki/download/attachments/3244619/ChIP-seq analysis with Cistrome tools.png"/>
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Here you need to choose analysis type and cistrome internal data and click Setup. For treatment tags only analysis type the following workflow appears:

 

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  <img src="/wiki/download/attachments/3244619/ChIP-seq analysis with Cistrome tools_1.png"/>
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For treatment and control tags analysis type the following workflow appears:

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  <img src="/wiki/download/attachments/3244619/ChIP-seq analysis with Cistrome tools_2.png"/>
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To run these workflows you need to select input annotations, and output files and directories. Also, if required, you can change parameters of MACS, CEAS, Conservation Plot, SeqPos, Peak2Gene, and Gene Ontology. Use the workflow wizard to guide you through the parameters setup process. The first wizard page appears automatically after the Setup button has been pressed or click Show wizard button on the Workflow Designer toolbar to open it:

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<center>
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  <img src="/wiki/download/attachments/3244619/ChIP-seq analysis with Cistrome tools_3.png"/>
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The first wizard page:

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