The question about regenerating a HiC contact map for the final assembly

[qdu-beep]

Hello developer,

After successfully running the Step1 and Step2, I got the two files ( out_JBAT.FINAL.agp and out_JBAT.FINAL.fa). I want to regenerate a .hic file corresponding to the final assembly. I'm not sure if the input files I chose to complete the Step 3 are correct ( the original BED/BAM file, contigs.fa.fai, out_JBAT.FINAL.agp and out_JBAT.FINAL.fa.chrom.sizes). I would be very grateful if you could provide some help! my commands are as follows.

Step1. juicerbox.sh

/software/HapHiC/scripts/../utils/juicer pre -a -q 1 -o out_JBAT samblasterHiCfilter2.bed scaffolds.raw.agp asm.fa.fai >out_JBAT.log 2>&1
(java -jar -Xmx32G /software/HapHiC/scripts/../utils/juicer_tools.1.9.9_jcuda.0.8.jar pre out_JBAT.txt out_JBAT.hic.part <(cat out_JBAT.log | grep PRE_C_SIZE | awk '{print $2" "$3}')) && (mv out_JBAT.hic.part out_JBAT.hic)

Step2. After adjusting in juicerbox

/software/HapHiC/scripts/../utils/juicer post -o out_JBAT out_JBAT.review.assembly out_JBAT.liftover.agp asm.fa

Step3. Regenerating a HiC contact map for the final assembly

(/software/HapHiC/scripts/../utils/juicer pre samblasterHiCfilter2.bed out_JBAT.FINAL.agp asm.fa.fai | sort -k2,2d -k6,6d -T ./ --parallel=8 -S32G | awk 'NF' > alignments_sorted.txt.part) && (mv alignments_sorted.txt.part alignments_sorted.txt)

(java -jar -Xmx32G /software/HapHiC/scripts/../utils/juicer_tools.1.9.9_jcuda.0.8.jar pre alignments_sorted.txt out.hic.part out_JBAT.FINAL.fa.chrom.sizes) && (mv out.hic.part out.hic)