I have cuffdiff files including control and treated FPKMs, log2 fold change, p-value, q-value, test stat. and significance values . To select differentially expressed genes (up/down regulated genes) respect to fold change, I would like to know whether I should only select those genes with q- values<0.05 ( q-value cutoff )?

Thank you in advance

The threshold for considering a fold change significant is arbitrary (but usually the q-value below 0.05 is used)