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  • Normalizing RNA-seq within samples

    Hi all,

    I have RNA-seq from different tissues (one RNA-seq for each tissue) and I would like to know for specific genes if and how they are expressed within my samples ( no need to compare between the tissues) . I thought to use TPM / FPKM but I am not sure how the RNA composition bias mentioned in DESeq and EdgeR user guide will affect my results in case I have a low expressed gene I am interested in.

    What method of normalization I should use?

    Thanks in advance!

    Best,
    Moriah

  • #2
    If you're worried about RNA composition bias, I would try using a series of non-depleting dual labelled molecular indices. You can then count and compare within your samples using the diverse set of labels. This is described further in this publication: http://www.pnas.org/content/early/2011/05/06/1017621108

    - Genohub

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    • #3
      Thanks for your answer!

      I already have the RNA-seq I just want to know how to normalize it to overcome the compositional bias...

      Comment

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