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igvteam / juicebox.js

HiC contact matrix visualization
MIT License
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chromogram: draft vs hi-c improved assembly #307

Closed ersgupta closed 5 years ago

ersgupta commented 5 years ago

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?

dudcha commented 5 years ago

Hello ersgupta.

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

Olga

ersgupta commented 5 years ago

Hey Olga, Thanks a lot. :)

Saurabh

ersgupta commented 5 years ago

Two points:

  1. 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.
  2. The output file contains same color (0,0,0) for all scaffolds. It seems this is not taken into account in the script.
jrobinso commented 5 years ago

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

dudcha commented 5 years ago

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

ersgupta commented 5 years ago

Hi @jrobinso sure. Will do. :)