chromogram: draft vs hi-c improved assembly

[ersgupta]

Hi Olga,

I am trying to use the supp/make-rainbow-tracks-assembly.sh script to make tracks.bedpe file to visualise the chromogram (similar to Fig 1 from Dudchenko et al 2017). I have couple of points regarding this, could you please address these?

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.

Thanks Saurabh

[dudcha]

Hello Saurabh,

1. the script you are pointing to is not relevant in this case. The rainbow track is created from the chrom-length assembly to draft. Make sure you are passing the chrom-length as ref.assembly and original draft assembly as draft.assembly

2. annotation color is not the rainbow color. The color is the next column, from 0 to 1. You can map it to continuous color however you want.

Olga

[ersgupta]

Thanks.

1. Got it, will try that.
2. So you mean, I can assign the color for each chromosome in annotation color column and the next column takes care of the gradient, right?

Saurabh

[dudcha]

Saurabh,

Chromosome-length assembly in this script is assumed to be a continuous gradient from 0 to 1 (for the first -c <ref_chrom_number> scaffolds). The relevant column says how the draft assembly should be colored in terms of this gradient.

Olga

[ersgupta]

Thanks Olga, I will try it out and get back to you.