------------------------------------------ 安装fastqc---------------------------------------------------
1）下载：http://www.bioinformatics.babraham.ac.uk/projects/download.html
2）
------------------------------------------ 安装tophat---------------------------------------------------
1）wget https://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.Linux_x86_64.tar.gz
2) tar xzvf tophat-2.1.1.Linux_x86_64.tar.gz
3) mv tophat-2.1.1.Linux_x86_64/ tophat2
调用./tophat2的时候会报错，
这个是因为我默认版本是python3的问题，需要将以下文件 #!/usr/bin/env python 该为#!/usr/bin/env python2.7即可。
需要修改的文件有：bed_to_juncs，contig_to_chr_coords，sra_to_solid，tophat-fusion-post*
4) echo 'export PATH=/home/jxdong/biosoft/tophat2/:$PATH' >>~/.bashrc
5)source ~/.bashrc
------------------------------------------ 安装hisat2--------------------------------------------------
1）wget http://www.ccb.jhu.edu/software/hisat/downloads/hisat-0.1.6-beta-Linux_x86_64.zip
2) unzip hisat-0.1.6-beta-Linux_x86_64.zip
3) cd hisat2-2.1.0/
4) echo 'export PATH=/home/jxdong/biosoft/hisat2-2.1.0/:$PATH' >>~/.bashrc
5)source ~/.bashrc
------------------------------------------ 安装cufflinks---------------------------------------------------
1)wget http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.Linux_x86_64.tar.gz
2)tar cufflinks-2.2.1.Linux_x86_64.tar.gz
3) mv cufflinks-2.2.1.Linux_x86_64/ cufflinks
4)echo 'export PATH=/home/jxdong/biosoft/hisat2-2.1.0/:$PATH' >>~/.bashrc
5)source ~/.bashrc