1 tophat官方网址：http://ccb.jhu.edu/software/tophat/tutorial.shtml
2 安装bowtie2：https://sourceforge.net/projects/bowtie-bio/files/bowtie2/
3 安装tophat参考：http://blog.sina.com.cn/s/blog_751bd9440102v4lq.html
Install quick-start
Download and extract the latest Bowtie 2 (orBowtie) releases.
Note that you can use either Bowtie 2 (the default) or Bowtie (--bowtie1)and you will need the following Bowtie 2 (or Bowtie) programs in your PATH:
bowtie2 (or bowtie)
bowtie2-build (or bowtie-build)
bowtie2-inspect (or bowtie-inspect）
cd
tar xvfz tophat-2.0.0.Linux_x86_64.tar.gz
cd ~/bin
ln -s ~/tophat-2.0.0.Linux_x86_64/tophat2 .
Now you can start the new version of TopHat with thetophat2command, while the previous version, if present, can still be launched with the regular "tophat" command (assuming this is how you used it before).
安装过程遇到问题：
出现错误行
tophat2 --help
File "/home/andengdi/lyr/app/tophat-2.1.1.Linux_x86_64/tophat", line 1003
except getopt.error, msg:
^
SyntaxError: invalid syntax
这种错误的解决方法参考：http://blog.sina.com.cn/s/blog_6c9eaa1501014x4z.html
解决方法：添加2.7，tophat的注释行改成 #!/usr/bin/python2.7（这个要看python2.7在哪里）；
解决之后：
