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-   -   RnaSeq differential expression (http://seqanswers.com/forums/showthread.php?t=34949)

Gorbenzer 10-30-2013 03:02 AM

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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