Errors using HiCExplorer HiCPlotTADs

I am trying to plot TADs using the HiCPlotTADs tool in, but I keep receiving the same error.

usage: hicPlotTADs --tracks tracks.ini --region chr1:1000000-4000000 -o image.png
hicPlotTADs: error: one of the arguments --region --BED is required

There is no place to upload a BED file in the --region argument and I am confused about how to get past this error. I have tried uploading my domain file (a BED file) using the gene track/BED track with no success. I am uploading my h5 matrix file (corrected) and the TAD domain file, which is what it seems like I should be doing. Please help me get past this error.

I am trying to visualize TADs so that I can compare them across two different arrangements in flies.

1 Like

Welcome, @Flies

I’m wondering if the “Boundaries file (optional)” input needs to be used, too. Maybe it is required or a duplicated function … but I’d like to get this working for you first, if possible.

What happens if you input a file for that option instead? Or in addition?

Please let us know if that works or not. If you want to put example data into a new history, try a rerun in there, then share it back, we can take a closer look with the wrapper authors. Examples help when tool bugs are suspected, and this sounds like one so far. You should also submit a bug report for the error. Put a link to this topic in the comments for extra context. Troubleshooting errors


Hi @jennaj,

Thanks for your reply!

I get the same error when I input a file into the boundaries parameter as well. I will try with example data and share it back. Hopefully we can get through this quickly.

You need to fill the “Region of the genome to plot”
Could you confirm it solves the issue?

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Hi @Flies – I misinterpreted the error message that you posted back – sorry to complicate it :upside_down_face:

Please try what @lldelisle suggests instead. She is one of our developers. With your own data is fine to start with, then you can try with tutorials if something goes wrong to troubleshoot more or just to learn more about how this tool suite works.