Could I just use tophat to map my reads and cuffdiff to deal with the bam file and get the DEG?

Yes. You can. Since you already have gtf file, you don't need to do the reference-based transcriptome assembly. 

Good luck.

Thanks,O(∩_∩)O~~

To work with Cufflinks you may need to understand each step on this workflow:

http://cole-trapnell-lab.github.io/cufflinks/manual/

DEG are generated on the last step Cuffdiff and the plot are visualized in R using cummRbund. The advantage using Cufflinks is normalization is done directly by Cuffdiff.

Here are the command line to use the workflow. If you are not familiarized with them, you may consider use Galaxy.

It is best to go through all the steps. 

Dear Zhang,

I suggest you have to execute the steps strictly tophat followed by cufflink, cuffmerge and cuffdiff to get appropriate DEGs.