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:
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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.
Environment requirements:
Before proceeding, please make sure that your computer is configured as follows:
The following software packages are installed:
Make sure R and Python are added to the PATH environment variable.
Move directory “cistrome” from the Cistrome Configuration Package, that goes with this tutorial, to the “data” subdirectory of the UGENE installation directory.
Install required Bioconductor packages. To do it, please make sure your computer is connected to the internet, unpack “installRpackages.R” script from the Cistrome Configuration Package and run it as follows:
- On Linux/Mac OS X open a terminal and run commands:
- “sudo Rscript –vanilla installRpackages.R”
- It may be required to also run the following command on Linux:
- “sudo apt-get install libxml2-dev”
- On Windows search for “cmd” executable file, select “Run as administrator” item in its context menu and run command:
- “Rscript –vanilla installRpackages.R”
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Download and install the UGENE NGS package to use this pipeline. |
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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