Rezwan Tariq

Sorry for the late reply because I was traveling and busy with field experiment. I used these commands for the assembly #1st command ``` module load hifiasm/0.19.8 hifiasm -o yellow_assembly...

@tallnuttrbgv I have an idea from the previous publications. Just run the hifiasm with the default settings, e.g., --n-hap 2. Then use your primary assembly and perform the chromosomal scaffolding...

Hi @zengxiaofei I used hifiasm with following command and got these outputs ``` module load hifiasm/0.19.8 hifiasm -o yellow_assembly -t 32 --hom-cov 63 \ --h1 yellow_1.fastq.gz \ --h2 yellow_2.fastq.gz \...

@zengxiaofei thank you so much for helping. I will let you know soon after getting the results.

Hi @zengxiaofei following the above given suggestions. I have this output in form of 44 groups. The groups are shown here in the hic plot. So what do you suggest...

@zengxiaofei thank you for your great help. I will add the final figure here after correction with juicebox as reference for other users as well.

@zengxiaofei Please check this plot having 44 chromosomes. How does this look? [contact_map.pdf](https://github.com/zengxiaofei/HapHiC/files/15090765/contact_map.pdf)

One more question, why these red circled lines are not contacting to the main scaffolds? I tried to make their curation but didn’t work. Is it due to artifacts of...

@zengxiaofei thank you so much for your great support, and shared shared examples will be helpful to improve my genome plot accordingly.