Cphasing plot signal loss

[Micranthes]

When I use Juicebox for more complex operations, such as splitting a contig that is mounted incorrectly, after exporting a new review.assembly, I find that there is a loss of Hic signals when I redraw it.

Raw plot

I removed a bug mount of contigs in the middle, and redrew it with the following code:

# code
cphasing utils assembly2agp ${sample}_${hap}.review.assembly -n 12
cphasing agp2fasta ${sample}_${hap}.review.agp 	${sample}_${hap}_rwa.fa > ./${sample}_${hap}.fa
cphasing-rs contigsizes  ${sample}_${hap}.fa > ${sample}_${hap}.contigsizes
cphasing pairs2cool ${sample}.pairs.gz   ${sample}_${hap}.contigsizes  ${sample}_${hap}.10k.cool
cphasing plot -a ${sample}_${hap}.review.agp -m ${sample}_${hap}.10k.cool -o ${sample}_${hap}.review.png --whitered

Redraw

Difference in assembly section before and after modification
Before:

After:

[wangyibin]

Sorry for my late reply.

This error might stem from inconsistent input; the contig name should consistent among ${sample}_${hap}.review.agp, ${sample}_${hap}.contigsizes and ${sample}.pairs.gz.

In this sense, you should use the contig sizes from raw.fa to generate the cool file.

[Micranthes]

Thank you, I'll give it a try