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zengxiaofei / HapHiC

HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data
https://www.nature.com/articles/s41477-024-01755-3
BSD 3-Clause "New" or "Revised" License
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[p_utg] Stange Hi-C maps after diploid scaffolding from polished hifiasm unitigs #85

Open Isoris opened 1 month ago

Isoris commented 1 month ago

Hello Xiaofei,

I have used HapHic at MAPQ1 NM < 3 as explained in the front matter page, the initial contigs were from the p_utg.fa and the --gfa file used was the corresponding gfa file.

image `

make BWA index

bwa index CMAM.asm.hic.p_utg.fa

map HIC reads

bwa mem -5SP -t 200 CMAM.asm.hic.p_utg.fa HiC_R1.fastq.gz HiC_R2.fastq.gz | samblaster | samtools view - -@ 14 -S -h -b -F 3340 -o HiC.bam

Filter aln for MAPQ 1 & Edit DISTANCE < 3

./HapHiC/utils/filter_bam HiC.bam 1 --nm 3 --threads 200 | samtools view - -b -@ 200 -o HiC.filtered.bam

SCAFFOLD with 2 rounds of error correction without inter-allelic links, GFA-based

./HapHiC/haphic pipeline CMAM.asm.hic.p_utg.fa HiC.filtered.bam 54 --gfa "CMAM.asm.hic.p_utg.gfa" --remove_allelic_links 2 --correct_nrounds 2`

After assembly it seems that the resolution of scaffolds failed somehow, any idea why this happened? Thank you in advance.

zengxiaofei commented 1 month ago

Your result seems to be fine, just import the .assembly file and double click on the contact map.