------------------------------------------ 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