JiaYi Liang
JiaYi Liang
Dear developer, hello, I have some questions I'd like to ask! I am currently using verkko to assemble a homologous hexaploid using only HiFi data. The verkko strategy combining HiFi...
Hello, I followed the steps below for analysis, but `pb-CpG-tools.combined.bed` is empty. Why is this happening? I am using `Revio ccs.bam`. Could there be any mistakes in my commands that...
I obtained the result file HiTE.full_length.gff. How should I interpret this? I previously saw that it was determined based on cov>0.95. Can I directly consider these as intact TEs? If...
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...
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...
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 \...
Hello, I would like to know which steps before EDTA can be split for processing. I have a 28G genome. Based on my guess: The LTR step inherently supports parallel...