Juicebox
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aidenlab
Visualization and analysis software for Hi-C data -
**Describe the bug** When you begin to move around a chr or a scafold, you have a blank region that appear in the map. When you pass the cursor in...
**Describe the bug** I start to update juicebox from 1.11 to 2.16. The newer version is much faster; it is great. The *.hic + *.assembly generated by 3d-dna can be...
Hi, i want to know the detail information about `.assembly ` file. For example, could you tell me some details like `.hic` data format. in my view, the `.assemly` file...
Dear Aiden lab, Thank you for this great tool. Looks like the latest released jar files are susceptible to log4j vulnerability (https://www.kb.cert.org/vuls/id/930724), would it be possible to generate release with...
Hi, I'm scaffolding a quite large plant genome (estimated 4.1 Gbp). I've used hifiasm to get an initial assembly from PacBio HiFi reads, and then 3d-dna pipeline to get initial...
**Describe the bug** I am attempting to compare two .hic files -- one from 4DN portal and one locally generated. The files differ when loaded together and the output depends...
Dear Colleagues, I tried to edit a 3D-DNA assembly using JBAT. Both v1.9.8 and v1.11.08 were downloaded to my Macbook Pro and tested. After loading the hic and Final.assembly file,...
Hi, I'm wondering how to load a mouse gene annotation file to Juicebox when visualizing contact maps. Thanks!
**Describe the bug** The result of getSumFactor is inverted. This bug can change the results of the later analysis using KR-normlized count data. **Code** getSumFactor should return "Square root of...
Hello! I used to use juicebox_ 1.11.08, it works normally, but the speed is really very slow. I found that you released the new version of juicebox.2.13.05, but I've been...
