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yeeus / GCI

A program for assessing the T2T genome continuity
MIT License
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Uniform window size for visualization #4

Closed comery closed 6 months ago

comery commented 6 months ago

hi developers,

I noticed in a case, the overall picture looks different from a zoom-in picture of a specific region. I guess this is because you use an adopted window size for different plots with different scales. Making it uniform will be better to compare each other.

image

yeeus commented 6 months ago

yeah that's a good suggestion. I have editted the window size as a constant value (50Kb) in the new version (v0.3). I think that would help.

comery commented 6 months ago

Why did you close the issue so quickly? Be patient! I used the newest version of GCI, but I got the new error as report as the following:

The length of plotting region (15706) is less than the window size (50000)

Do you have any ideas?

yeeus commented 6 months ago

I'm sorry for that. Anyways, I think the problem was caused by the plot funcion which would generate plots for every chromosomes and coincidentally, your genome assembly has a chromosome (or contig) less than the window size (50Kb by default). You can lower the window size or using the latest version of plot_depth.py in the directory utility with the option -R which would generate plots only for the sepcific regions.