Juicebox takes very long to load assembly file

[Joan Jong]

Hi Olga,

I have some problem loading the final.assembly file into Juicebox as it takes a very long time. When it manages to load the file, the program freezes up when I double-click to zoom in. I have tried allocating 15GB to the application but the problem still persisted. I am able to load the tutorial assembly from http://dnazoo.org/methods. More details are listed below:

• Machine used: macOS Big Sur, version 11.2.3
• Memory available: 16GB
• Juicebox version: 1.11.08
• Final.hic file size: 877.3MB
• Final.assembly file size: 2.4MB

I think my hic and assembly files are very large. May I ask if there are alternative ways to do post-review without going through Juicebox? Thank you.

Cheers,

Joan

[Olga Dudchenko]

Hey Joan,

How big is your assembly file? Note that in many cases if you have a lot of very small bits there is this thing called bundling that you can use to help. Look it up in the Genome Assembly Cookbook. Note that if you are using dev version of JBAT the bundling is done automatically.

Hope this helps,

Olga

[Olga Dudchenko]

P.S.: Oh sorry, ignore the question about assembly file size, I can see it now in your post. Automatic bundling happens whenever assembly file is >1Mb. Bundling should definitely help.