Zhougeng Xu

ERROR: Raw TIR results not found in Fhispida.fasta.mod.EDTA.raw/Fhispida.fasta.mod.TIR.raw.fa

5

Hi, shujun I recently run the EDTA pipeline(v2.0.1) on the Ficus hispida using the following command > As the EDTA was running successfully on my arabidopsis species, the pipeline was...

Enhancement of CPU/juicer.sh in error judgement of genomePath

1

**Describe the bug** In `https://github.com/aidenlab/juicer/blob/master/CPU/juicer.sh`, it use ` if [ -z "$genomePath" ]` to judge whether the genomePath is set or not , but even you set the unexisted file...

non-numeric argument to binary operator

1

I want to show all sequence in one page, but the following code will not work ```r nt_seq

I write a `edit-fasta-according-to-new-cprops.py` which do the same thing as `edit-fasta-according-to-new-cprops.awk` and generate the same results. I have used `cmp` to compare the results of edit-fasta-according-to-new-cprops.py and edit-fasta-according-to-new-cprops.awk .The results...

Compile error: no matching function for call to ‘safeTestForEach(

1

I use the following command to compile this software ``` git clone https://github.com/ggonnella/gfaviz cd gfaviz/ qmake-qt5 make ``` And an error throw out ``` g++ -c ogdf/basic/extended_graph_alg.cpp -std=c++11 -I. -O3...

ALLHiC optimize可以跳过GA吗

2

我在使用ALLHiC组装简单的二倍体时发现，optimize这一步可能会将原来正确的朝向搞错 这是使用optimize默认参数绘制的热图  根据信号强弱变化，左下角的方向可能是反了  于是我试着optimize 用 --skipGA跳过GA步骤结果绘制的热图  结果可能更加符合预期 我想问的是 1. GA步骤是如何根据clm文件确定contig的朝向呢？ 2 GA步骤是否是必须的？

Question about the input of `pyscenic ctx`

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Hi, Could you please give a further instructions on the **database_fname** of `pyscenic ctx`, as I encountered an error when use following command base on the [turtorial]( https://github.com/aertslab/SCENICprotocol/blob/master/notebooks/PBMC10k_SCENIC-protocol-CLI-tracks.html) ```bash pyscenic...

how to prepare motif2tf file for `path_to_motif_annotations` in plant

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Hi, I'm trying to use SECNICPLUS in my plant species recently, but I'm having problems. Referred to https://scenicplus.readthedocs.io/en/latest/human_cerebellum_ctx_db.html, I create a motif database for my species, but I encountered a...

第一步，配置一个wsl，详细版本见[http://xuzhougeng.com/archives/building-a-wsl-based-python-data-science-environment](http://xuzhougeng.com/archives/building-a-wsl-based-python-data-science-environment)，如下是简明版 首先，得确保自己的操作系统符合要求，对于windows11直接就可以了，对于Windows 10 ，要求高于version 2004 或高于Build 19041，可以通过打开powershell运行如下命令确认。 ```Python Get-ComputerInfo -Property "OsName", "OsVersion", "WindowsProductName", "WindowsEditionId", "OsHardwareAbstractionLayer" ```  接着，在powershell中运行如下`wsl --install`, 跟着提示操作就可以，中间可能需要重启一下电脑。 默认情况下，WSL使用宿主机的一般内存，例如你的电脑配置是16G内存，那么WSL最多就用8G。如何修改见详细版。 第二步，在WSL中安装conda, 我用的是清华镜像提供的Miniconda ```Bash wget https://mirrors.tuna.tsinghua.edu.cn/anaconda/miniconda/Miniconda3-py38_4.12.0-Linux-x86_64.sh bash Miniconda3-py38_4.12.0-Linux-x86_64.sh ``` 根据提示安装结束后，重新打开wsl，就可以进行下一步。...

AttributeError: 'Search' object has no attribute 'args'

1

运行日志如下 ``` 2024-05-18 18:41:34,471 INFO worker.py:1540 -- Connecting to existing Ray cluster at address: 10.10.87.98:6379... 2024-05-18 18:41:34,480 INFO worker.py:1715 -- Connected to Ray cluster. View the dashboard at 127.0.0.1:8265 2024-05-18...