RnaSeq differential expression

[Gorbenzer]

Hi everyone,
It's time to use our IonTorrent to evaluate difference in trascription when our bacteria are grown in different conditions.

Wiki gives a nice overview of different softwares and getting the reads quality filtered and then aligned to a reference genome should not be a big problem (fastQC and BWA should do ok).

When coming to analysis i didn't found enough informations on what are the best options for our needs. Can you provide some suggestion for:

- Normalization through KPRM (or maybe is better DESeq?)
- Evaluation of promoters/trascription start of the genes
- Differential expression/comparison of expression level of samples of the same strain growth in different conditions.
- Identification of non-coding RNAs

Thanks so much to everyone that will help