1 依赖软件：bowtie，bowtie2，samtools，boost c++ library
2 建立索引文件：
bowtie包括bowtie，bowtie-build，bowtie-inspect
bowtie2包括bowtie2，bowtie2-build，bowtie2-inspect，默认会找bowtie2
bowtie-build运行结果会得到一些.ebwt的文件
bowtie2-build建index，运行结果得到一些.bt2文件：
bowtie2-build genome.fasta genome
3 santools依赖库：ZLIB_1.2.3.3，需要更新libz.so.1版本，zlib-1.2.3 版本不够高，需要安装1.2.8版本zlib，安装路径：/data_center_01/soft/zlib-1.2.8/libz.so.1，添加到bashrc的LD_LIBRARY_PATH中
4 boost c++ library：CPLUS_INCLUDE_PATH=$CPLUS_INCLUDE_PATH:/data_center_01/home/NEOLINE/lihang/Programe/Package/boost_1_55_0/include/
4 tophat下载：官网：http://ccb.jhu.edu/software/tophat/index.shtml
tophat使用参考经典protocol文章：Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks