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Hi,
When I run the haphic pipeline, it occurs the following error:
```
(haphic) [cuixb@yls allhic]$ ~/tools/biosoft/HapHiC-main/haphic pipeline -h
Traceback (most recent call last):
File "/home…
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Hi @tangerzhang,
As you mentioned in https://github.com/tangerzhang/ALLHiC/issues/93, after generating the wrk_dir directory with the script partition_gmap.pl, ALLHiC_prune can be executed individu…
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Dear colleague,
I get an error in the pipeline during Juicer pre and perhaps related to juicer tools. I use conda in an ubuntu 22.04
This is the input
(hic-scaffolding) jpons@tesla:~/Downloads…
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Hi @sc-zhang!
I am trying to use ALLHiC_prune. However, it kept generating "Segmentation fault (core dumped)" in "Getting contig pairs" step
I am using below version as environment.
```
gcc | 9.…
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Dear Professor Zhang,
After partition chromosome with ALLHiC_partition.py, I got a fasta file and a bam file for each chromosome, respectively. Although I try the script allhic_extract.sh, optimize.…
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Hi @lemene,
I hope you are well.
I have just tried PECAT with our ONT data from a plant genome, it worked like a charm, and I got the best primary assembly ever! Thank you very much for your bri…
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The ALLHiC_Prune program caused my file system to fill out fast and eventually crash it be filling all 1TB space available. I downloaded new version from the ALLHiC_components website and the size of…
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Hi,
I got 2 haplotypes of a simple genome using hifiasm(https://github.com/chhylp123/hifiasm) with HiC data, and I want to know how to anchor these two haplotypes to chromosome-level using allhic. …
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您好！
您这个ALLHiC软件要想鉴定contigs之间的等位基因，需要一个contigs的注释文件和cds文件。也就是说需要对contigs进行从头注释得到这两个信息文件，才能鉴定等位基因，从而去除染色体之间的噪音，是这样吗？
因为我这里看来，做一个大的基因组，注释是非常消耗时间和计算资源的，我在想怎么只通过已经发表的cds序列blastn到contigs上，来鉴定contigs之间的等位基…
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Hi, I am trying to assemble haplotype genome using ALLHiC. I am puzzled by the partition.pl step using Allele.gene.table. And I find the alternative partition_gmap.py. So I have two questions:
1. I…