Should I combine RNA-Seq results from two sequencings

[szy0931]

I am doing bacteria RNA-Seq with Illumina HiSeq.
I did the experiment twice with the same strains.
Each experiment has 3 biological replicates for each strain.
Now I have results from the two experiment.
Should I combine the results for analysis from the step of Cuffmerge?
Thank you!

[bastianwur]

You have the same experiment twice?
To what do you want to compare it to?

[Macspider]

Before merging them I would go with some statistical test to see their closeness. For example, run cufflinks on both separately and then do a principal component analysis (PCA) with R to see how close the results are.

But first: why do you say that they are two experiments with 3 replicates each? Does this mean that they are two different conditions? In that case, if you merge them you lose information, unless you want to do a gene prediction and thus you need all in one file.