chromogram: draft vs hi-c improved assembly

Question

chromogram: draft vs hi-c improved assembly

Closed this issue 5 years ago · 6 comments

Hi, is there a script using which I make plot chromograms like in Fig1 of Dudchenko et al. 2017 to show a comparison from the old to improved assembly?

Answer 1 · 2019-07-16T16:09:16.000Z

Hello ersgupta.

This is a 3D-DNA script: https://github.com/theaidenlab/3d-dna/blob/master/supp/make-rainbow-tracks-assembly.sh

Olga

Answer 2 · 2019-07-16T17:32:02.000Z

Hey Olga,
Thanks a lot. :)

Saurabh

Answer 3 · 2019-07-16T21:06:57.000Z

Two points:

I get an error saying that I have annotations which span multiple contigs. I see that you have a *-w-split.awk to take care of this. However, this needs to be changed in one line in make-rainbow-tracks-assembly.sh. I made the respective change and the error goes away.
The output file contains same color (0,0,0) for all scaffolds. It seems this is not taken into account in the script.

Answer 4 · 2019-07-16T21:08:32.000Z

Hi @ersgupta , this issue is not about juicebox.js, @dudcha where is the proper forum for this?

Answer 5 · 2019-07-16T21:09:34.000Z

@ersgupta Please move this to 3D-DNA issue board or aidenlab.org/forum.html.

Answer 6 · 2019-07-16T21:12:28.000Z

Hi @jrobinso sure. Will do. :)