Assembly > Import Map Assembly Option
Closed this issue · 7 comments
Hello
Thank you for sharing your useful toolbox.
I am wondering if juicebox.js has an option similar to Assembly > Import Map Assembly option in the Juicebox desktop GUI app which can be used to add a .assembly file obtained from an AGP file using the agp2assembly.py script (https://github.com/phasegenomics/juicebox_scripts). The desired effect is a 2D annotation showing the assembled scaffolds as shown in the attached figure.
Cheers
Usman R.
No it does not. For 2D annotations the "bedpe" format is supported.
Are you using juicebox.js as an embedded component, or loading from a juicebox-web instance (such as the one at aidenlabe.org/juicebox?
Thank you.
I am using juicebox.js as an embedded component.
In that case you might configure a 2D track like this
"tracks": [
{
"url": "https://www.dropbox.com/s/d2in3505qbekzx0/merged_loops.bedpe?dl=0",
"name": "merged_loops.bedpe"
}
]
It is described here: https://www.ncbi.nlm.nih.gov/assembly/agp/AGP_Specification/
The relationship between that and bedpe is not obvious, some scripting will probably be involved.