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Mapping the dynamic genetic regulatory architecture of HLA genes at single-cell resolution
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<article id="post-Mapping the dynamic genetic regulatory architecture of HLA genes at single-cell resolution" class="h-entry article article-type-post" itemprop="blogPost" itemscope itemtype="https://schema.org/BlogPosting">
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<a class="p-name article-title" href="/2023/12/18/Mapping%20the%20dynamic%20genetic%20regulatory%20architecture%20of%20HLA%20genes%20at%20single-cell%20resolution/">Mapping the dynamic genetic regulatory architecture of HLA genes at single-cell resolution</a>
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Mapping the dynamic genetic regulatory architecture of HLA genes at single-cell resolution
（一）单细胞数据集
69个滑膜样本
22个肠样本
91个PBMC体外培养样本
OneK1K cohort
（二）Pseudobulk cell type specific eQTL
由于作者关注HLA基因，所以只对相关的髓系细胞、T细胞、B细胞进行了分析
不同cohrt构建不同的PEERs，根据不同群体大小使用不同数量的PEERs
随后单独对每个cohort进行eQTL mapping (P < 4e-9)，找出每个HLA基因对应的lead eQTL，其中91.7% (88/96)具备mean directional concord-ance，证明了不同cohort间存在一致性。
最终分析得到24个与MHC关联的lead eQTL
For each cohort:
Eresid=βGXG+sex+age+βi(1,2,...,5)PCi(1,2,...,5)+β...
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MAGMA
简介
MAGMA is a tool for gene analysis and generalized gene-set analysis of GWAS data. It can be used to analyse both raw genotype data as well as summary SNP p-values from a previous GWAS or meta-analysis.
原理
待施工
安装
官网提供了如下版本
即开即用
使用
示例数据
GWAS数据：BMI meta analysis的一套数据，样本量为339224
基因坐标：Gene locations, build 37
1KG：European
通路文件：msigdb.v7.4
01 Annotation
需要提供对下载得到的GWAS summary statistics进行预处理，得到snp.loc文件，\t分割，分别为rsID chrosome postion，不需要列名：
123cat gwas.tsv | \ awk -F'\t'...
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<a class="p-name article-title" href="/2023/11/09/cloudpan189-go_usage/">天翼云盘命令行工具cloudpan189-go的使用</a>
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cloudpan189-go Usage
repo直达 https://github.com/tickstep/cloudpan189-go
简介
天翼云盘CLI，基于GO语言实现。仿 Linux shell 文件处理命令的天翼云盘命令行客户端。
下载
在发布页面下载系统对应安装包，解压即可使用，这里以amd64为例
1234wget -c https://github.com/tickstep/cloudpan189-go/releases/download/v0.1.3/cloudpan189-go-v0.1.3-linux-amd64.zipunzip cloudpan189-go-v0.1.3-linux-amd64.zipcd cloudpan189-go-v0.1.3-linux-amd64./cloudpan189-go
执行上述步骤会显示如下内容：
使用
查看帮助
1cloudpan189-go > help
登录
输入login命令，会提示输入用户名与密码
1cloudpan189-go > login
查看文件列表
1clou...
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Autobangumi Usage for Mac
配置qBittorrent
宿主机配置
首先需要打开WebUI选项，允许远程连接使用，同时设置用户名与密码，勾选对本地主机上的客户端跳过身份验证：
创建Autobangumi下载目录，需要在qBittorrent默认下载目录下创建，本机设置的默认下载目录为/Users/wenjichen/Downloads，所以要在/Downloads下创建：
1mkdir /Users/wenjichen/Downloads/Autobangumi
创建数据和配置文件夹
创建Autobangumi container挂在目录：
123# 使用 bind mountmkdir -p ${HOME}/AutoBangumi/{config,data}cd ${HOME}/AutoBangumi
拉取镜像运行容器
12345678910111213docker run -d \ --name=AutoBangumi \ -v ${HOME}/AutoBa...
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堡垒机自动登录脚本
前言
使用组里服务器要先连接所里服务器堡垒机，再连接到组里服务器，两个密码还不一样，还都是强密码，根本记不住（大悲:(，原来一直用着Terminus集成管理，虽然有连接后执行命令的功能，但是仍无法实现一步到位连接组里服务器，后查询可使用expect脚本实现。
实现
实用expect脚本
1234567891011121314151617181920#!/usr/bin/expectset timeout 30spawn ssh wenjichen@xxx.xxx.xxx.xxexpect { # stimulate input jump server password "(wenjichen@xxx.xxx.xxx.xx) Password:" {send "xxxxxxxxxx\n";exp_continue} # stimulate select server "请选择目标资产：" {send "2\n";exp_continue&...
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<a class="p-name article-title" href="/2023/11/04/10yearsGWASbyBroadInstitute/">After a decade of genome-wide association studies, a new phase of discovery pushes on</a>
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十年的全基因组关联研究正在推进新的发现诞生——通过检测遗传突变，科学家将揭开疾病发生的根源，并为精准医疗铺平道路
原文标题：After a decade of genome-wide association studies, a new phase of discovery pushes on
原文副标题：By probing genetic variation, scientists continue to unearth the roots of disease and pave the way for precision medicine
译者：温继晨
追寻常见疾病的遗传根源，本质上是为了更好地预防与治疗疾病。由于我们无法得知疾病发生的根本原因，当今用于治疗常见疾病的药物遵从对症下药，而非针对发病根源。拿糖尿病举例，常见的治疗方式是使患者控制较低水平的血糖，但是这种方法无法解决导致胰岛素β细胞受损或胰岛素抵抗（胰岛素作用的靶器官对胰岛素作用的敏感性下降）的根本功能障碍。
通过研究揭示疾病的生物机制，进而发现常见遗传性疾病的基因根源，这种思路能够为准确识别患病风险较高的...
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Singularity Usage
官方文档：https://docs.sylabs.io/guides/3.2/user-guide/cli.html
简介
待施工
拉取外部容器
1singularity pull QTLtools.sif docker://naotokubota/qtltools
拉取外部容器后进行更改
待施工
运行容器
类命令行工具的运行容器
1singularity exec bind /pmaster/wencjien/sceQTL:/pmaster/wenjichen/sceQTL QTLtools.sif QTLtools pca --vcf 012/chr21.filter.vcf.gz --scale --center --distance 50000 --out pca/chr21.filter
交互式运行容器
1singularity shell QTLtools.sif
Rerference
Singularity日常使用
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seqkit usage
Repo直达 https://github.com/shenwei356/seqkit
Introduction
seqkit是重庆医科大学病毒性肝炎研究所副研究员沈伟老师基于Go语言开发的跨平台的、快速的、全面的fasta/q处理工具
Installation
1234# Generalconda install -c biconda seqkit# Alternative for macbrew install seqkit
Usage
Example file: AARS.lncRPI.bed
Description: AARS蛋白结合lncRNA位点信息
Source: POSTAR3 from LuLab@Tsinghua Univeristy
subseq
Get subsequences by region/gtf/bed, including flanking sequences.
Usage:
seqkit subseq [flags]
Flags:
–bed string by tab-delimit...
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