Regarding HIC signal loss

[linyuiz]

I ran the following commands to generate the .hic file, but I encountered a loss of HIC interaction signals. Why is this happening?

cphasing-rs pairs2mnd -q 0 ../HiC.clean.pairs.pqs -o HiC.clean.pqs.mnd.txt
cphasing utils agp2assembly ../cphasing_output/4.scaffolding/groups.agp -o groups.assembly
# cphasing utils assembly2agp groups.review.assembly -o groups.review -n 19:2
# cphasing utils agp2fasta groups.review.agp -o groups.review.fasta
ln -sf $(ls *.pqs.mnd.txt) used.merge_no_dups.txt
export LD_LIBRARY_PATH=''
bash /project//scripts/.scr/scripts/software/3d-dna/visualize/run-assembly-visualizer.sh -p true -q 0 groups.assembly used.merge_no_dups.txt;

[wangyibin]

Hi,
Please check the heatmap generated by the plot command to see whether these blank regions are present.

[linyuiz]

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 -bs ${heatmap_binsize} -oc

Running it this way or adding the --low_memory parameter doesn't work either, there will still be missing HIC signals.
Whether it's the q0 or q1 results, this white signal will appear.
Could it be that there were already blank signals in the files under the HiC.clean.pairs.pqs folder from the beginning? Maybe I should use bwa alignment instead of chromap?

My general order is as follows:

cphasing pipeline -f used.genome.fa -pcd $pore_c -t $threads -n 0:2 -hcr -p AAGCTT

Is the parameter setting -p AAGCTT the cause of this blank signal?

[wangyibin]

Hi,
Sorry, this may be a bug in the pqs file.

Can you replace the pqs file with pairs.gz to run cphasing pairs2cool? If the blank regions still exist, then the issue is not caused by the pqs file.

cphasing pairs2cool `../HiC.clean.pairs.gz` \
        ../used.genome.contigsizes HiC.clean.q${min_quality}.${cool_binsize}.cool \
        -q ${min_quality} -bs ${cool_binsize}

Is the parameter setting -p AAGCTT the cause of this blank signal?
The parameter -p AAGCTT will not affect the heatmap results.

You can also add my QQ (738339463) to help us locate this bug

Best,
Yibin

[linyuiz]

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 HIC.filtered.bam file obtained from HapHIC through bwa alignment and filter_bam filtering, converted it into a pairs.gz file, and now the plots under 5.plot/ are functioning normally without any blank signals.