Bulk RNA-Seq转录组学习

与之对应的是single cell RNA-Seq，后面也会有类似文章。

参考：https://github.com/xuzhougeng/Learn-Bioinformatics/

作业：RNA-seq基础入门传送门

资料：RNA-seq Data Analysis-A Practical Approach(2015)

Bioinformatic Data Skill

biostar handbook

A survey of best practices for RNA-seq data analysis

Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis

Detecting differential usage of exons from RNA-seq data

转录组入门（1）: 工作环境准备

miniconda2

cd src
wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
bash Miniconda2-latest-Linux-x86_64.sh

conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/msys2/
conda config --add channels bioconda
conda config --set show_channel_urls yes

在里面安装各种工具

conda create -n biostar sra-tools fastqc hisat2 samtools htseq

 

转录组入门(2)：读文章拿到测序数据

AKAP95 regulates splicing through scaffolding RNAs and RNA processing factors. Nat Commun 2016 Nov 8;7:13347. PMID: 27824034

GSE81916，https://www.ncbi.nlm.nih.gov/geo/

for i