CPhasing
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wangyibin
C-Phasing/CPhasing: Phasing and scaffolding polyploid genomes based on Pore-C, HiFi-C/CiFi or Hi-C.
您好， Collapse是一个非常好的模块，我组装的是一个同源性较高的多倍体植物，Collapse区域我一直不知道怎么处理。之前我尝试了通过gfa和ont数据（depth）来进行Collapse区域的恢复。但是在这过程中我发现有一个Collapse区域一直没有被恢复。 通过我的经验来看，2号染色体的黑框框起来的部分应该是同时和1和3号染色体的部分区域发生了Collapse，该区域的测序深度应该约为正常的测序深度3倍（正常的测序深度约为20X），结果也是这样的，下图是该区域中一个contig的深度图。 无论是基于gfa还是ont数据进行Collapse的恢复，该区域的contig都没有成功的生成新的拷贝（或者说被成功的恢复），通过查询过程文件，contigs.collapsed.contig.list统计的Collapse区的contig中是存在该区域的conitg的，但是运行“cphasing collapse rescue”后，生成的collapsed.rescue.contigs.list文件中却没有该区域的Contig，最终导致这些contig不能成功的被恢复。这个问题是什么导致的？是否是因为并非是2个染色体发生了坍塌，而是3个染色体，导致这些contig不知道应该分配到那些cluster中？
老师您好！感谢您发布的CPhasing软件！我最近正在用它测试组装的单倍型基因组，我遇到了一些错误不知道应该怎么解决，还望老师可以给一些建议！ 这是我的运行命令： ``` export PATH=/media/APP/miniconda3/bin/:$PATH export PYTHONPATH=/media/APP/python3.12/site-packages:$PYTHONPATH export PATH=/media/APP/CPhasing/bin:$PATH export PYTHONPATH=/media/APP/CPhasing:$PYTHONPATH cphasing pipeline -f genome.fasta -hic1 HiC_1.fq.gz -hic2 HiC_2.fq.gz -t 40 -n 47 ``` 我遇到的问题是在第三步： ``` #----------------------------------# # Running step...
Hello, Thank you for devoloping such good tool for polyploid genome assembly. Now I am assembling a tetraploid plant genome (AABB) with two closely related subgenomes using HiFi and Hi-C...
I used both cphasing and haphic for plotting, and I noticed that the plots generated by haphic have a KR mode with darker colors, while the ones from cphasing appear...
Hi, this is a great tool. I was trying to understand how it uses the data. Is CPhasing able to utilize the multiple connections between long read proximity ligation (HiC...
I couldn't find parameters for setting image dimensions（**height and width**）in the help documentation: https://wangyibin.github.io/CPhasing/latest/zh/CLI/plot/#parameters-of-plot. Additionally, for genomes with smaller chromosomes like mine, I can only use **--no-ticks** to prevent overlapping...
Hi, I hope this email finds you well. I am very interested in using Cphasing for my research on an allotetraploid species and wanted to reach out for some clarification....
I ran the following commands to generate the .hic file, but I encountered a loss of HIC interaction signals. Why is this happening? ```shell cphasing-rs pairs2mnd -q 0 ../HiC.clean.pairs.pqs -o...
my plot.cmd.sh: ```shell min_quality=1 cool_binsize=10k heatmap_binsize=500k if [ ! -f HiC.clean.q${min_quality}.${cool_binsize}.cool ]; then cphasing pairs2cool ../HiC.clean.pairs.pqs \ ../used.genome.contigsizes HiC.clean.q${min_quality}.${cool_binsize}.cool \ -q ${min_quality} -bs ${cool_binsize} fi cphasing plot -a ../4.scaffolding/groups.agp \...
老师，您好： 当我使用cphasing-rs pairs-break生成新的 corrected.pairs.gz文件时，发现少了一个输入文件，我该怎么得到这个文件呢，此前我已经使用cphasing scaffolding命令得到了一个新的corrected.groups.agp文件 命令1：cphasing scaffolding ../3.hyperpartition/output.clusters.txt ../2.prepare/A.poreC.counts_AAGCTT.txt ../2.prepare/A.poreC.clm.gz -sc ../2.prepare/A.poreC.split.contacts -f ../A.raw.assembly.fa -t 120 --corrected -o corrected.groups.agp -m precision 命令2：cphasing-rs pairs-break -t 120 -o corrected.groups.agp ../A.poreC.paf.gz cphasing-rs pairs-break...
