I have set of differentially expressed gene files. I need to figure out if a specific histone is associated with changes in their promoters.
Is there a specific galaxy tool similar to annotation hub in R available.
Please suggest
1 Like
Try the tool: AnnotateMyIDs (a function from Bioconductor’s R AnnotationHub) to see if that contains the data you want. See the supported organisms on the tool form.
- The tool is available at the public server Galaxy EU https://usegalaxy.eu now.
- We plan to add it to the public server Galaxy Main https://usegalaxy.org soon.
- The tool can also be installed into your own Galaxy server from the Main Tool Shed.
To access more R functions, or those not specifically wrapped by a tool, try: Visualize > Interactive Environments.
- This will allow you to launch a Jupyter notebook with an existing Docker image available that includes R (and other packages), at both of the above public servers.
1 Like
Thanks a ton , this was very helpful
1 Like
This helped me to annotate my gene, but which tool I used to get the epigenetic peaks . Please suggets
The question is a bit broad with the given info, but how to get, produce, analyze epigenetic data (are many types!) depends on your organism, data providers that support it (for pre-computed or raw data eg: ENCODE and others), what kind of data you already have or decide to link in, the tools that will work with it, larger goals.
- Search Galaxy resources/discussion with the keywords “epigenetics galaxy”
- Galaxy Public servers, including those hosting Epigenetic tools. Some have their own tutorial/guides/publications.
- Galaxy Tutorials
- Have a look at the resources published here by EpiGene for a nice overview of data sources/providers.
Tips:
- Any data can be uploaded into Galaxy using the Upload tool and some resources have tools under Get Data where you can search for data and download it into Galaxy directly.
- Review the Galaxy ToolShed for the tools are you interested in working with to see if they are wrapped already. There is a specific Epigenetic category.
- Tools that are not wrapped could be, by yourself, by making a request to the IUC, or in collaboration with them.
- For R functions not wrapped into tools, the interactive environment can be used. If the current Docker image does not have what you needed (tool, data), you could suggest that it be added by the IUC.
- IUC Gitter chat https://gitter.im/galaxy-iuc/iuc and tool development at GitHub https://github.com/galaxyproject/tools-iuc. They can also help you find domain-specific Galaxy tool developers if something new/novel is wanted - you’ll need to be clear about your larger goals, current data, and the like.
Very simple answer with many assumptions, as an example, that can all be done within Galaxy.
For a human gene list or genome coordinates of regions of interest for those genes: review the UCSC > ENCODE data tracks. The raw data is available for use in peak calling tools plus they have a few tracks specific to histone markers targeted at promoters and other regulatory elements. Peaks (generated by them, or by you from the raw data) could then be compared to genes/genomic coordinates/regulatory regions of interest. Up/down-expression overlapping with marker peaks could then be investigated with a tool suites like DeepTools and HiCExplorer.
1 Like
Thank you so much. Your knowledge is awesome.
2 Likes