search

zengxiaofei / HapHiC

HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data
https://www.nature.com/articles/s41477-024-01755-3
BSD 3-Clause "New" or "Revised" License
142 stars 10 forks source link

How to add/remove elements to a haphic plot? #20

Closed zhengyanstu closed 6 months ago

zhengyanstu commented 7 months ago

Hello, @zengxiaofei Thank you for developing this software. I am new to Haphic and have some questions about the plot function.I ran the following command: haphic plot out_JBAT.assembly.agp HiC.filtered.bam --bin_size 500 --min_len 5 --normalization log10 --border_style outline & The generated plot is attached. 1 I am wondering how to generate a plot with group information on the y-axis, similar to the example you provided. Thank you for your help.

zengxiaofei commented 7 months ago

Hi @zhengyanstu,

You need to input out_JBAT.FINAL.agp instead of out_JBAT.assembly.agp. And I always recommend using KR normalization rather than log10.

Best regrads, Xiaofei

zhengyanstu commented 7 months ago

Hi @zhengyanstu,

You need to input out_JBAT.FINAL.agp instead of out_JBAT.assembly.agp. And I always recommend using KR normalization rather than log10.

Best regrads, Xiaofei

Thanks for your reply. I generated out_JBAT.hic and out_JBAT.assembly using 'bash juicebox.sh' in the 04_build directory. After export them to Juicebox, I found that the original assembly results were good, so I just chose the out_JBAT.assembly.agp. Do I need to modify the sequence names when using Juicebox to import a reviewed assembly file and then use Juicer to generate an agp file?(If I want to set the scaffold name) I chose KR normalization at the beginning, but the background of the plot was too cluttered. Is there any way to solve this? image

zengxiaofei commented 7 months ago

After export them to Juicebox, I found that the original assembly results were good, so I just chose the out_JBAT.assembly.agp.

If you want to visualize the original scaffolding result, you should choose scaffolds.raw.agp, not out_JBAT.assembly.agp.

Do I need to modify the sequence names when using Juicebox to import a reviewed assembly file and then use Juicer to generate an agp file. (If I want to set the scaffold name)

If you want to set the scaffold name, you can modify the first column in scaffolds.raw.agp to change the scaffold names, or modify the texts in a PDF editor (e.g., Adobe Illustrator). To regenerate an agp file after manual curation in juicebox, please refer to the detailed example I provided in another issue.

I chose KR normalization at the beginning, but the background of the plot was too cluttered.

It's a color range issue, which is controlled by two parameters, --vmax_coef and --manual_vmax. You can manually adjust them to achieve a better heatmap. Setting --manual_vmax 0.01 may be suitable for your case.