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  • RnaSeq differential expression

    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

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