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Hello,
I would like to ask what do you usually do when encountering this type of patterns in the scaffolds:
![image](https://github.com/user-attachments/assets/c66139df-15e4-4083-8799-7a67334cdb…
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Hi,
I am trying to assemble a phased genome of an outcrossing hexaploid grass species. The hybrid assembly failed with the error "hifiasm: gfa_ut.cpp:14200: uint32_t load_scaf_base(all_ul_t*, char*…
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I run the second script for Hi-C Pro after the bowtie2 alignment and the script seems to have problem processing all the files (in the "Merge chunks from the same sample" and "Generate binned matrix …
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Hi, thank you for the great program.
Do you have any recommendations, advice, or considerations for using mHi-C with Hi-C datasets generated with the _in situ_ DNase Hi-C protocol (which uses DNa…
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Hi,
I successfully assembled an _A. thaliana_ genome for which I obtained two partially phased haplotypes of size 148.1 Mb (hap1) and 146.4 Mb (hap2), respectively. These files are in **.fasta** f…
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while hi-c jumping is not included we should not allow to use both hi-c and trio in the same run.
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HELLO.
my out.JBAT.log file generated is empty.
(java -jar -Xmx32G juicer_tools.1.9.9_jcuda.0.8.jar pre out_JBAT.txt out_JBAT.hic.part
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Thanks for your excellent software, Could you provide the benchmark script for promoter capture Hi-C dataset as your paper has described?
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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.
![imag…
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I really interested in your code on works of analysis cells. But when I check your code, there is one important function missing: find_periodicity, would it be possible to upload it？ Thanks, Carey.