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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
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