Normalizing RNA-seq within samples

[tamari]

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

[Genohub]

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

[tamari]

Thanks for your answer!

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