hicBuildMatrix seeting for restriction cut file or a bin size


I attempted to follow the tutorial (Hands-on: Hi-C analysis of Drosophila melanogaster cells using HiCExplorer / Epigenetics) for conducting HiC analysis. In the tutorial, it suggests selecting a “Bin size” for analysis. According to the previous discussion, I should choose version 3.4.0, but I can only find version Are these two versions the same? Since my program stalls indefinitely, I am unsure whether I selected the correct tool.

Best regards,

HI @Sheng-Chieh_Hsu

Hum, I’m not sure which is best. I did notice that the tutorial is not technically supported at the public Galaxy sites, and instead just in a docker image. How to get that docker is described at the bottom of the tutorial and working in that would give the most exact reproduction of the current methods.

Screen Shot 2024-03-04 at 1.17.17 PM

That said, I’ve used this tool successfully before at all three of the UseGalaxy servers.

This is a fresh test using the tutorial data and workflow. Maybe you can use it as an example / answer key? https://usegalaxy.eu/u/jenj/h/galaxy-workflow-galaxy-hi-c

And, just to clarify:

  • Bin size: this is a scientific metric available as an option on the tool form, and is used for clustering your data. I’m not sure what you mean by “stalls” but you could explain more about what is going on.

  • Tool version: this is a name for a specific version of the wrapper around the tool. Differences between tool versions can include different options on the form, or different organization of options, and sometimes a different version of the underlying 3rd party tool (modified algorithm).

“Bin size” is an example of an option/parameter on a tool form, and different versions of tool forms might have that in different places.

Let’s start there. You should be able to see and import the history I shared, and the workflow itself is available on the tutorial homepage if you want to grab that too. Find all of the other input data at the same Zenodo record as the first two inputs.