Question: RNAseq Normalization for eQTL Mapping?
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gravatar for QVINTVS_FABIVS_MAXIMVS
5 weeks ago by
USA SoCal
QVINTVS_FABIVS_MAXIMVS2.2k wrote:

How do you normalize RNAseq data for eQTL mapping?

I have 200 samples with bulk RNAseq data, from that I generated matrix of TPM values for each gene. I also have a matrix of expected alignment counts and a matrix of read counts.

I suppose I should use TPM for the eQTL mapping. If so, how do I normalize the values? Do I perform a quantile normalization or some other method? Should I even normalize the TPM matrix?

Additionally, what TPM cutoff should I apply and should I exclude genes according to X% of samples with TPM expression over Y_TPM_CUTOFF?

Thanks!

ADD COMMENTlink written 5 weeks ago by QVINTVS_FABIVS_MAXIMVS2.2k

It will likely depend on the eQTL program that you're using and the type of data distribution that it expects. Which one are you aiming to use?

ADD REPLYlink written 4 weeks ago by Kevin Blighe37k
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