Xiaofei Zeng

> > > > 我最后还是解决了这个问题，代码应该没什么问题，主要还是显存、内存、swap其中之一不足。保证swap空间足够，降低cpu和device memory limits就好了。 > > > > > > > > > 请问怎么解决的？ > > > > > > 就如我前面说的，保证显存+内存+硬盘剩余空间足够应该就能跑起来。 比如我显存4G、内存16G的笔记本，device limit设置的3.5G，ram limit设置的10G，最后保证C盘的空间足够就可以。 > > 谢谢，我的笔记本就是4+16的，但是我device...

It's very normal. Current scaffolding tools cannot guarantee perfect results. Manual adjustment in Juicebox is typically necessary. In addition, there are also other reasons that may lead to poor results....

Close this issue as there has been no response for two weeks.

In some cases, `haphic plot` may not able to get a suitable color range automatically due to a strong background of inter-scaffold Hi-C signals. In such scenarios, please set the...

Note: If you only change the `--manual_vmax` parameter, you do not need to rerun `haphic plot` using the BAM file. Instead, you can just use the `contact_matrix.pkl` file instead, which...

We recommend not to link these unanchored contigs into a scaffold (chrUn) as you have done, because it is not a true scaffold and could be misleading. Instead, we prefer...

I have added a new parameter `--specified_scaffolds` in haphic plot in the latest [commit](https://github.com/zengxiaofei/HapHiC/commit/ecab25640df90c523812cec6da7dd7a5502523b1) . You can specify the scaffolds to visualize by using something like: `--specified_scaffolds "group1,group2,group3,group4"`

In both cases, the `nchrs` parameter should be set to 22. Because there should be two sets of haplotypes in allhaps.fa or p_utg.fa. > Additionally, what is the difference between...

@DayTimeMouse Yes.

> In your experience, would you recommend using haphic for chromosome-level assembly in this case? I usually do not consider heterozygosity as a direct reference metric because different methods and...