Xiaofei Zeng

Hi @amvarani, As far as I know, SALSA is currently the only tool that utilizes BED files. There is no widely used aligner for Hi-C/Pore-C data that outputs alignments in...

Thank you for sharing this valuable information. You have convinced me, and I will make this update when I have time. Best wishes!

Yes, you are correct. For your primary or haplotype-collapsed assembly, please set the `nchr` as 13.

Hi Rongfeng @melop, Overall, there are two main strategies for scaffolding haplotype-resolved assemblies (hap*.p_ctg). The first is aligning all Hi-C reads to each haplotype and scaffolding them separately. Although this...

> Hi Xiaofei, I'm wondering if it would be possible to develop a tool to compare the agp files produced by both strategies and merge them together, so that you...

> if I rephrase my question: is there a way to identify genomic regions where the two haplotypes agree or disagree from HiC data? If so, one could partition the...

the same problem

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。

> > 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。 > > 竟然还需要 swap，我服务器上 swap 都是默认关的😂 其实我是在windows上装的，程序会在个人目录下.cache里生成临时文件，RAM够的情况下，保证这部分磁盘空间充足应该就ok。linux应该也一样，保证对应生成临时文件的目录空间足够就好，在RAM足够的情况下也用不上Linux意义上的"swap"

> > 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。