JiaYi Liang

Thank you for your reply. I do have a contig genome with HIFI+ONT, but I still want a version with the HIFI-Only strategy. If it's really not possible to change...

Another question: Why is there **no black border** in the drawn image when I clearly set **--add-hap-border**? ```shell cphasing plot -a rawname.agp -m Bam.q${mapq}.q0.10k.cool -o hic_plot.png -bs 500k -oc --dpi...

```shell 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 ${cool_binsize} fi cphasing plot -a ../4.scaffolding/groups.agp \ -m HiC.clean.q${min_quality}.${cool_binsize}.cool \ -o groups.q${min_quality}.${heatmap_binsize}.wg.png...

```shell cphasing bam2pairs $bam_file -q 0 -o sample.pairs.gz && cphasing pipeline -hcr -f $genome -prs sample.pairs.gz -t $threads -n 19:2 ``` I have already solved this issue. I used the...

Thank you for your reply. I still want to know if splitting the genome into 50M segments with a step size of 500K for Anno_SINEv2 and TIR-Learner will have any...

Currently testing a 1G genome, the time spent on each part is as follows: All tasks are run with -threads 6, with 3 parallel tasks during execution. ``` RepeatModeler2 RM2(-quick):...

> Thank you for your reply. I still want to know if splitting the genome into 50M segments with a step size of 500K for Anno_SINEv2 and TIR-Learner will have...

> Hi, I'm very sorry for the delay in my response. Can you provide more detailed information for this error, such as the log of `cphasing-rs pairs2mnd`. I also encountered...

Resolved: ```shell ##please use: cphasing-rs pairs2mnd -q 0 ../01.C-Phasing/cphasing_output/pore-c.pairs.pqs/ -o pore-c.pqs.mnd.txt ##don't use: cphasing pairs2mnd ../01.C-Phasing/cphasing_output/pore-c.porec.gz -q 0 -o sample.mnd.txt ```

It seems that as long as the 0.95 threshold is met, it will be classified as an intact TE? Also, isn't 0.95 quite strict? EDTA seems to use 0.9 as...