Assembly > Import Map Assembly Option

[GallVp]

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.

[jrobinso]

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?

[GallVp]

Thank you.

I am using juicebox.js as an embedded component.

[jrobinso]

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"
                }
            ]

[GallVp]

Thank you @jrobinso

Do you know any tool which can convert AGP files to BEDPE?

[jrobinso]

I don't, @nchernia @sa501428 any ideas?

Is the AGP format described somewhere?

[GallVp]

It is described here: https://www.ncbi.nlm.nih.gov/assembly/agp/AGP_Specification/

[jrobinso]

The relationship between that and bedpe is not obvious, some scripting will probably be involved.