如何解决cuffdiff运行结果中表达量为0的情况？
cuffdiff -o cdiffout -b ref.fasta -u -p 15 --library-type fr-firststrand \
-L H_3,O_3,F_3 cuffmergeout/merged.gtf \
tophatout/H-1-3/accepted_hits.bam,tophatout/H-2-3/accepted_hits.bam,tophatout/H-3-3/accepted_hits.bam \
tophatout/O-1-3/accepted_hits.bam,tophatout/O-2-3/accepted_h its.bam,tophatout/O-3-3/accepted_hits.bam \
tophatout/F-1-3/accepted_hits.bam,tophatout/F-2-3/accepted_hits.bam,tophatout/F-3-3/accepted
_hits.bam解决办法：先使用 cuffquant 对每个样本估计 gene 和 transcript 的表达量，然后再用 cuffdiff 进行差异表达的分析。
原理是：distribute your computational load over a cluster；save your time.