Differential gene expression (RNA Seq analysis MiSeq paired end reads 250 bp)

[Irshad]

Hi All,

I am relatively new to bioinformatics, therefore your expertise could help me how to go about RNA Seq analysis.
I have two (Bacterial) experimental conditions (control and assay), three time points (T1, T2 and T3) and three replicates for each condition at each time point.
I want to analyze the RNA seq data and if possible find differentially expressed genes (upregulated or downregulated).
Can someone suggest me what tools to use to get the job done? What to use for quality trimming of the sequences??
for analysis Bowtie, Tophat, Cufflinks or DESeq??
Your response in this regard will be highly appreciated.

With best regards
Irshad