转录组分析(2) - 软件安装

conda环境创建

conda create -n py3 python=3.8
conda create -n py2 python=2.7

数据预处理软件

conda activate py3 # 激活py3环境
conda search fastqc # 查询fastqc依赖的python版本
conda install fastqc # 安装fastqc
conda search multiqc # 查询multiqc依赖的python版本
conda install multiqc # 安装multiqc
conda search fastp # 查询cutadpter依赖的python版本
conda install fastp # 安装fastpHisat-

数据处理软件

Tophat-Cufflink-Cuffdiff

conda search tophat   # 查询tophat依赖的python版本
conda install tophat   # 安装 tophat
conda search cufflinks   # 查询cufflinks依赖的python版本
conda install cufflinks   # 安装 cufflinks
conda deactivate

HISAT-StringTie-Ballgown

conda activate py2
conda search hisat2
conda install hisat2
conda search stringtie
conda install stringtie
conda deactivate
sudo R

options(BioC_mirror="https://mirrors.tuna.tsinghua.edu.cn/bioconductor")
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("ballgown")

Subread-featurCount-DEseq2

conda activate py3
conda search subread
conda install subread
conda deactivate
sudo R

options(BioC_mirror="https://mirrors.tuna.tsinghua.edu.cn/bioconductor")
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("DESeq2")