###因为gtf和fastq的对应关系，从igenome上打包下载所有hg19的信息##

1. tophat2比对

tophat2 -p 15 -G ../reference/hg19/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf -o **_out ../reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome **_1.fastq **_2.fastq

2.cufflinks组装转录本

cufflinks -g ../../reference/hg19/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf -o ** -p 10 **.bam

3.cuffmerge合并转录本

###其中assembly.txt包含所有要合并的gtf文件的路径####

cuffmerge -g ../reference/hg19/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf -s ../reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa -p 15 assembly.txt

4.cuffdiff差异表达分析

###labels之间用逗号隔开，重复的bam文件之间用逗号隔开#####

cuffdiff -o diffout/ -labels exp,control -p 10 -u merged_asm/merged.gtf **.bam **.bam