RnaChipIntegrator: integrated analysis of gene expression and ChIP data

Galaxy tool wrappers for running the RnaChipIntegrator program (http://fls-bioinformatics-core.github.com/RnaChipIntegrator/) for integrated analyses of gene expression and ChIP data.

There are two tools available that are built around RnaChipIntegrator:

• General RnaChipIntegrator tool that allows any peaks to be analysed against any gene list
• A "cannonical gene" variant which allows ChIP peaks to be analysed against a list of cannonical genes for different genomes

Automated installation

Installation via the Galaxy Tool Shed will take of installing the tool wrapper and the RnaChipIntegrator programs, installing the .loc files, and setting the appropriate environment variables.

Manual Installation

There are three files to install:

• rnachipintegrator_wrapper.xml (the Galaxy tool definition for general usage)
• rnachipintegrator_canonical_genes.xml (tool definition for the "canonical gene" variant)
• rnachipintegrator_wrapper.sh (the shell script wrapper)

The suggested location is in a tools/rnachipintegrator/ folder. You will then need to modify the tools_conf.xml file to tell Galaxy to offer the tool by adding the lines:

<tool file="rnachipintegrator/rnachipintegrator_wrapper.xml" /> <tool file="rnachipintegrator/rnachipintegrator_canonical_genes.xml" />

You will also need to install the RnaChipIntegrator program:

• http://fls-bioinformatics-core.github.com/RnaChipIntegrator/

In addition for the cannonical gene and histone modification variants, it's necessary to copy the .loc.sample files to .loc Galaxy's tool-data folder:

• Cannonical genes: its necessary to manually acquire cannonical gene list files from UCSC and then add appropriate references in the rnachipintegrator_canonical_genes.loc file.

If you want to run the functional tests, copy the sample test files under test-data to Galaxy's test-data/ directory. Then:

./run_tests.sh -id fls_rnachipintegrator_wrapper

How to get canonical gene data

Getting canonical gene info from UCSC is covered in the screencast at http://blog.openhelix.eu/?p=6097

In summary:

• UCSC genome browser: if multiple versions of each gene are visible (e.g. if you view 'human Feb 2009 GRCh37/hg19' positions chr17:41,100,000-41,300,000) then:
  • Scroll down to the Gene & Gene Prediction section
  • Click on the UCSC genes link
  • Uncheck the tickbox next to splice variants and resubmit to view without duplicates.
• UCSC table browser: to obtain the canonical set of genes from the table browser:
  • Select knownCanonical from the table menu
  • Select selected fields from primary & related tables from the output format menu
  • Click on Get output
  • Select the fields of interest (e.g. 'chrom', 'chromStart', 'chromEnd' from the 'knownCanonical' table plus 'geneSymbol' from the kgXref table.)
  • Click on Get output to get the data for download

(Hint: to also get strand direction information i.e. +/-, also allow selection from the refGene table, and select the strand field.)

History

Developers

This tool is developed on the following GitHub repository: https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator

For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use the package_rnachipintegrator_wrapper.sh script.

Licence (MIT)

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