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  • Should I combine RNA-Seq results from two sequencings

    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!

  • #2
    You have the same experiment twice?
    To what do you want to compare it to?

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    • #3
      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.

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