What is the process after mapping ?

[ugurcabuk]

Hi guys,

I have a raw data, which is rna-seq paired end. I have downloaded genome reference from ncbi. Then, I have mapped rna seq to genome reference through tophat2. I had some results like accepted.hits.bam. After this process, I used the cufflinks for assembly. Finally, I have a transcripts.gtf file. Firstly, I do not know how to interprate these files. Secondly, After all this process, What i should do ? I mean, What options do i have ?
Well, Should i use artemis or igv ? Actually i dont really know.

Thanks in advance,
your respectfully,

[gringer]

What is the question you are trying to answer by doing this mapping?