HiCexplorer usage

Hi all

I am planning to use HiC explorer. I have uploaded the data in the server and was planning to use the workflow, which is already given. I am unable to load the data in the workflow and my data cannot show it. Can anyone suggest/help me in this regard?


Hello, Your question may not be clear enough for someone to answer. Are you using https://hicexplorer.usegalaxy.eu/ or another server?

I think I understand that you are able to upload your files to galaxy and see your files as green blocks in your history. But this is unclear:

I am unable to load the data in the workflow and my data cannot show it.

Do you mean that you cannot select the files you uploaded as input? Did you checked if it is the correct file type?

HI. Thanks for the reply. Yes I am using https://hicexplorer.usegalaxy.eu/ . And you are right, I can see my files as green blocks in history. I have checked the workflow requirements and my data fits for that. If I try running individual tool, it will work, however, since the workflow has all the tools required, my data is not getting uploaded in workflow.

What is the name of the workflow?

  • From scratch to TAD and plotting

You need to upload you data as a collection with type list. In the upload window you will find the ‘collection’ tab at the top of this window. First you need to click the ‘start’ button and after uploading you can click the build button.

Here you can find more info:


And not sure but maybe another option is to import the workflow and change the input yourself.