What does this set of perpendicular lines mean? (not grid lines)

[TeresaPegan]

Hello,

I was wondering what is the significance of these red perpendicular lines, shown in the attached screenshot? The lines span the entire size of the genome window. There is only one set of the lines in my genome, and they cross in the middle of a large chromosome that has been assembled with HiC information from a lot of small scaffolds.

These lines do not seem to be information about HiC contacts. They change in relative size to the rest of the grid when I zoom in and out (as if they are created with vectors rather than information on the grid). However, when I change the color of the contact map, the line color changes too. These lines are present in one of two genome assemblies I am working with, but not the other.

I have not been able to make the lines go away using any of the options in the "View" part of the menu. I also have not been able to find anything on this issues page or the docs about lines like this, though I apologize if I've missed something.

I'm just curious what the lines are and whether they indicate anything I should know about my assembly. Thanks!

I am using juicebox with an assembly I processed with YaHS. To open the GUI I use Juicebox_1.11.08.jar with JDK 8 on a Mac laptop with Sequoia 15.2

[dudcha]

These are most likely parts of the genome that have a set of consecutive Cs or Gs and accumulate short reads which were sequences using illumina’s two color chemistry (which report no bases as Gs. If you do adapter and trimming and two-color chemistry handling you r just manually remove them these will go away.Please make sure you are citing the tool correctly: what you are using is Juicebox Assembly Tools aka JBAT.Thank you,OlgaOn Feb 16, 2026, at 7:41 AM, Teresa ***@***.***> wrote:TeresaPegan created an issue (aidenlab/Juicebox#1047) Hello, I was wondering what is the significance of these red perpendicular lines, shown in the attached screenshot? The lines span the entire size of the genome window. There is only one set of the lines in my genome, and they cross in the middle of a large chromosome that has been assembled with HiC information from a lot of small scaffolds. These lines do not seem to be information about HiC contacts. They change in relative size to the rest of the grid when I zoom in and out (as if they are created with vectors rather than information on the grid). However, when I change the color of the contact map, the line color changes too. These lines are present in one of two genome assemblies I am working with, but not the other. I have not been able to make the lines go away using any of the options in the "View" part of the menu. I also have not been able to find anything on this issues page or the docs about lines like this, though I apologize if I've missed something. I'm just curious what the lines are and whether they indicate anything I should know about my assembly. Thanks! I am using juicebox with an assembly I processed with YaHS. To open the GUI I use Juicebox_1.11.08.jar with JDK 8 on a Mac laptop with Sequoia 15.2 Screenshot.2026-02-16.at.8.23.38.AM.png (view on web) —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[TeresaPegan]

Thank you Olga, this is helpful!

It sounds like you are suggesting that these lines do represent mapped contacts -- that they are places where there are strong apparent contact rates across the entire genome (due to the artifactual GC content in 2-color Illumina machines.)

I still think the lines are unexpectedly even, if they represent HiC contacts. For example, I can see other horizontal and vertical lines throughout the grid that clearly show this kind of pattern, but they are a little pixelated-looking, as I would expect from some stochasticity in the mapping. But these two perpendicular red lines I am referring to display no variation across the whole window. I hope the attached screenshots demonstrate what I mean. Each new screenshot shows some pixelated-looking lines vertical lines in contrast to the completely solid and unvarying horizontal line -- which is the same as the horizontal line depicted in my screenshot above, although it appears much smaller in these new screenshots because I zoomed in.

Anyway, maybe GC artifacts are still the explanation, but I just wanted to check. Thanks!