iCAMP builds phylogenetic tree based on bin

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1

hello!
When I use the iCAMP process, I want to build a phylogenetic tree based on bin, but I have searched all over the iCAMP function and there is still no such function. How should I try it?

2

Hi @alex_123

The community had trouble understanding your question. Would you please explain more about what you are trying to do?

  1. Galaxy server URL
  2. Tool name/version (find at the top of the form)
  3. Describe what kinds of read data you have, and the current data formats
  4. If you are following a tutorial or known workflow, which? (reference by URL)
  5. The larger goal if that seems relevant

In general:

  • If you are looking for a tool, try searching the tool panel.
  • If you found the tool you want to use already, but the direct usage is not exactly what you want to do, is there a way to pre-process the data that helps? Example (guess!): filter different “bins” of data into separate files of a collection, then run the collection as a non-pooled batch.
  • If you are looking for a tutorial or template workflow, search our GTN training site. Example search: https://training.galaxyproject.org/training-material/search2?query=phylo
  • If you are looking for a workflow, search the Workflows area of a large public server with the expanded advanced search functions (EU, AU, US are good choices). These are now populated with WorkflowHub and other public sources, along with GTN.
3

Hi
I am using the IEG3 pipeline and want to create the following picture.
After analysis, it was found that the innermost layer of this picture is a tree based on phylogenetic signal division, not based on OTU/ASV.

image.png
image.png689×707 222 KB

Jennifer Hillman-Jackson via Galaxy Community Help <notifications@galaxy.discoursemail.com> 于2024年1月10日周三 08:42写道：

4

Hi @alex_123

It sounds like you will need to generate a track for that other data, and add it to your Circos visualization.

The person who runs this server posts dedicated tutorials on the server homepage, along with publication links, and since it is a custom pipeline, those are your best source of help. You could also write into them directly: find the contact email address also on the server homepage.

If they would like to join this forum and host discussions here, they are welcome to! We could also get them add them to the Galaxy Directory here: https://galaxyproject.org/use/

XRef: http://ieg3.rccc.ou.edu/

5

@alex_123 , were you able to find this ? I am having the same issue trying to build the rings with ecological processes.

6

Welcome @ChathuZ

The Galaxy server that offers this pipeline is for private use only. For issues using the tools, you’ll need to contact the server owner directly. The email contact is on the server homepage above.

The help I was able to give before was for general use of Circos: new tracks can be layered onto existing tracks. The baseline feature coordinates used are specific to each graphic and can be customized! Meaning, these could be OTUs, or chromosomes, or any other baseline feature you may be using to summarize other features against to produce a graphic.

What I can state that Circos requires very specific data formats! So, start by double checking your file formats if there are problems. The common data values between tracks should all use consistent labels. This includes the case of values. As an example, these would all be “different”: otu222 versus OTU222 versus OTU 222.

Hope this helps! :slight_smile: