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Download and install the UGENE NGS package to use this pipeline. |
The ChIP-seq pipeline “Cistrome” integrated into UGENE allows one to do the following analysis steps: peak calling and annotating, motif search and gene ontology. ChIP-seq analysis is started from MACS tool. CEAS then takes peak regions and signal wiggle file to check which chromosome is enriched with binding/modification sites, whether bindings events are significant at gene features like promoters, gene bodies, exons, introns or UTRs, and the signal aggregation at gene transcription start/end sites or meta-gene bodies (average all genes). Then peaks are investigated in these ways:
- to check which genes are nearby so can be regarded as potential regulated genes, then perform GO analysis;
- to check the conservation scores at the binding sites;
- the DNA motifs at binding sites.
Note that it is originally based on the the General ChIP-seq pipeline pipeline from the public public Cistrome installation on on the Galaxy workflow platform.
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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 configure wizard appears:
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<center> <br> <img src="/wiki/download/attachments/3244619/ChIP-seq analysis with Cistrome tools.png"/> <br> </center> |
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<center> <br> <img src="/wiki/download/attachments/3244619/ChIP-seq analysis with Cistrome tools_1.png"/> <br> </center> |
For treatment and control tags analysis type the following workflow appears:
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<center> <br> <img src="/wiki/download/attachments/3244619/ChIP-seq analysis with Cistrome tools_2.png"/> <br> </center> |
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> <br> <img src="/wiki/download/attachments/3244619/ChIP-seq analysis with Cistrome tools_3.png"/> <br> </center> |
The first wizard page:
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The dashboard will contain information about workflow: input and output files, all information about task.
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The work on this pipeline was supported by grant RUB1-31097-NO-12 from NIAID. |