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deeptools / HiCExplorer

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
https://hicexplorer.readthedocs.org
GNU General Public License v3.0
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Having Issues using HiCExplorer with .hic files generated from Juicer v2.0 #798

Open tonyjhlam opened 2 years ago

tonyjhlam commented 2 years ago

Hello,

I am having problems using .hic files generated using Juicer v2.0

Specifically: UnicodeDecodeError: 'utf-8' codec can't decode byte 0xaf in position 1: invalid start byte

This could possibly be because I think Juicer v2.0 might have a different .hic formatting (v9 format)?

Any help would be great.

Thanks, Tony

tonyjhlam commented 2 years ago

@sa501428

ISonets commented 2 years ago

Greetings! Same issue confirmed. As mentioned in one of the previous issues, no samtools and/or bedtools re-installation are able to resolve this issue. Please fix ASAP. Thanks in advance!

sa501428 commented 2 years ago

How does HiCExplorer handle/read .hic files? Easiest option would be to use the latest version of straw. Alternatively, details about the new format are in this repo.

joachimwolff commented 2 years ago

We use hic2cool. Must be fixed there.

RomeroMatt commented 2 years ago

Hi All, Any updates on this issue? I'm having the same issue and was wondering if anything was in the works or if using the straw option is the only option? Thanks! -Matt

tonyjhlam commented 2 years ago

@RomeroMatt From what I gathered, hic2cool is no longer maintained by the owners. HiCExplorer does not want to pick up support for new juicer v9 .hic format since they rely on hic2cool and would take concerted efforts to add support for v9 format. And Juicer does not want to provide a cross-compatibility flag option to downgrade their file format so that Juicer v2 output can be used with tools that are no longer actively maintained but have been working with the old juicer format.

I myself did try to work on the source code of hic2cool, but after some time it was not worth the effort. I've instead downgraded my Juicer to v1.6, so that I am still able to use 3rd party tools that are not within the Aiden lab ecosystem. It is a shame since the only tools that work with Juicer v2 are those within juicebox. So now we are stuck with the decision of upgrading to Juicer v2 (which would be nice to use since there are some large ENCODE initiatives that will be using Juicer v2 in the future) but not being able to analyze data outside of juicebox, or downgrade to Juicebox v1.6.

RomeroMatt commented 2 years ago

Hi @tonyjhlam thanks for the info! That is unfortunate, but I suppose I understand. Naive question, how did you download this version from github? Each time I try to download from github I get v2.0. Thanks again! -Matt

tonyjhlam commented 2 years ago

@RomeroMatt Really should be a question for the Juicer repo or juicer google group, rather than the HiCExplore repo. https://github.com/aidenlab/juicer/releases/tag/1.6

lldelisle commented 1 year ago

Hi, I proposed a solution in #821