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Hello author:
(1)bwa mem -5SP -t 80 Six_genome.bp.p_ctg.fasta Q-6-Hi_c_1.clean.fq.gz Q-6-Hi_c_2.clean.fq.gz | samblaster | samtools view - -@ 80 -S -h -b -F 3340 -o HiC.bam
(2)/home/export/online3/c…
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The error message is:
```
Loading sequence file...
Allocating Memory...
Initializing data structures...
Computing TR Model Statistics...
Scanning Sequence 5...Traceback (most recent call last):
…
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Dear zeng:
I need to assemble a homozygous tetraploid and perform genotyping. I plan to use "work with hifisam".
haphic pipeline p_utg HiC.filtered.bam nchrs --gfa p_utg.gfa.
My commond:
cat YZ4.…
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### Description of feature
only on the production branch please
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曾老师,您好!
我最近在组装一个小麦品种基因组,草图是用hifiasm软件组装得到的,下游HiC挂载用的是p_ctg.g组装版本。Hic数据比对用的是您推荐的bwa mem流程,挂载用的是One-line command,可以得到较好的挂载结果,21条染色体。用juicerbox对一些易位和倒位拼装错误进行了手动矫正,但重新画图后发现很多修改没有变化,重新画图代码:~/software/HapH…
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Ref workflow: https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/hicexplorer/workflows/
Ref IDC feedback: https://github.com/galaxyproject/idc/issues/53
Ref reported a…
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In the quality check stsp of HiC-Pro pipeline I am getting the following error:
Run HiC-Pro 3.1.0
--------------------------------------------
Friday 19 July 2024 03:22:02 PM IST
Run quality c…
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Hi there,
I am using pixy to calculate dxy.
However, all of the **avg_dxy** is NA. I believe that I may prepared my file incorrectly.
Please forgive me if my question is too naive.
This is how…
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Hello, I ran Juicer 1.6 on my fastq data and have .hic files. I also ran Hiccups.
I would like to find differential loops and am exploring how to do so using your package.
Is there way to directly…
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When running `vkoverhead -hic-only` the `hic_upload_memcpy_*` seem to run twice instead of just once. I couldn't tell if this was intentional and I'm missing why, or if it's unintended.
```
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