tophat

tophat -p 4 -G  filter.gtf

-o  /SRR222

/index

SRR222.fastq

tophat -p 4 -G  filter.gtf

-o  /SRR222

/index

SRR717.fastq,SRR718.fastq

tophat -p 4 -G  filter.gtf

-o  /SRR222

/index

SRR669_1.fastq

SRR669_2.fastq

Usage:
    tophat [options] <bowtie_index> <reads1[,reads2,...]> [reads1[,reads2,...]]
                                    [quals1,[quals2,...]] [quals1[,quals2,...]]

Usage:tophat [options]* <genome_index_base> <reads1_1[,...,readsN_1]> [reads1_2,...readsN_2]

查看tophat的帮助文件。