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gusevlab / fusion_twas

methods for functional summary-based imputation
http://gusevlab.org/projects/fusion/
GNU General Public License v3.0
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What is the best way to normalise RNA-seq data when running FUSION.compute_weights.R? #42

Closed Fei-Yang666 closed 2 years ago

Fei-Yang666 commented 2 years ago

Dear developer,

Can you please let me know the preferred normalisation method for RNA-seq data when running FUSION.compute_weights.R? logCPM or other method? I want to run TWAS for both gene level and transcript level but got confused about the data normalisation methods and do not know whether there is a recommended approach. It is quite important and very looking forward for your reply. Will appreciate that very much

many thanks,

Fei

sashagusev commented 2 years ago

Hi Fei, the expression normalization step is very project specific so we don't have a single recommendation. I would generally follow the same process you would use for eQTL discovery or take a look at the analysis workflow from the GTEx Consortium (https://gtexportal.org/home/documentationPage#staticTextAnalysisMethods).

Fei-Yang666 commented 2 years ago

Thanks very much for your response :)