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aidenlab / Juicebox

Visualization and analysis software for Hi-C data -
https://aidenlab.org/juicebox
MIT License
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Not able to edit .hic file in Juicebox #958

Closed sgr308 closed 3 years ago

sgr308 commented 3 years ago

Hi, I assembled a genome assembly using SALSA2 and generated a .hic file using this method: https://github.com/marbl/SALSA#generate-hic-file-from-salsa-scaffolds

Then, I generated .agp and .assembly files using "makeAgpFromFasta.py" and "agp2assembly.py" from juicebox_scripts. https://github.com/phasegenomics/juicebox_scripts/tree/master/juicebox_scripts

First, I loaded .hic file and then I loaded .assembly file in Juicebox_1.11.08. The upload of both files completed without any error and I can see the Edit, Chr and Scaf on the right side but I am not getting the blue, yellow and green lines which I can see in this video at 2:00 minutes (https://www.youtube.com/watch?v=Nj7RhQZHM18).

The current .hic shows 21 scaffolds while I am expecting 19 scaffolds as this species contains 19 chromosomes. I can provide you the .hic and .assembly file for any troubleshoot.

Thanks, Sagar

dudcha commented 3 years ago

Hello Sagar,

We do not offer any support for Salsa since we are not developers of that tool: my guess would be that the hic file is not in the right ‘assembly’ format.

Thanks, Olga

On Jun 1, 2021, at 7:00 PM, Sagar Patel @.***> wrote:

 Hi, I assembled a genome assembly using SALSA2 and generated a .hic file using this method: https://github.com/marbl/SALSA#generate-hic-file-from-salsa-scaffolds

Then, I generated .agp and .assembly files using "makeAgpFromFasta.py" and "agp2assembly.py" from juicebox_scripts. https://github.com/phasegenomics/juicebox_scripts/tree/master/juicebox_scripts

First, I loaded .hic file and then I loaded .assembly file in Juicebox_1.11.08. The upload of both files completed without any error and I can see the Edit, Chr and Scaf on the right side but I am not getting the blue, yellow and green lines which I can see in this video at 2:00 minutes (https://www.youtube.com/watch?v=Nj7RhQZHM18).

The current .hic shows 21 scaffolds while I am expecting 19 scaffolds as this species contains 19 chromosomes. I can provide you the .hic and .assembly file for any troubleshoot.

Thanks, Sagar

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tinyfallen commented 1 year ago

Hi @dudcha

I meet the same issuse, the .hic file with black lines could not be edit. Could you please tell me how to convert it to a right ‘assembly’ format?

Many thanks!