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。