tophat运行指令如下： [code]nohup tophat2 -p 10 -o ~/desktop/tophat_result/model ~/desktop/mm10/mm10_index ~/desktop/cleandata/mmhcRNA-model.read1_Clean.fastq.gz ~/desktop/cleandata/mmhcRNA-model.read2_Clean.fastq.gz > ~/desktop/tophat_result/model/tophat_log 2>&1[/code]log文件见截图 [attach]306[/attach] 有想过可能是index本身的问题，重建一次以后依然是这个情况，bowtie2版本为2.2.5     关于cufflinks的安装问题，系统为macOS 10.13。大致流程是按照： [url]https://github.com/cole-trapnell-lab/cufflinks[/url] 的流程来的。其中samtools在用命令行手动安装完成以后，根据其描述要在本机路径里面复制一次sam tools的binary，用于给cufflinks提供一个bamlib。按照文中提供的操作以后，在安装cufflinks并进行./configure操作时，提示 [quote] checking for bamlib... configure: error: We could not detect the bam libraries (version  or higher). If you have a staged bam library (still not installed) please specify $BAM_ROOT in your environment and do not give a PATH to --with-bam option.  If you are sure you have bam installed, then check your version number looking in . See http://randspringer.de/bam for more documentation. [/quote] 不知道有使用mac的大佬这一块是怎么解决的