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mbasugit / Imputation

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Input data #2

Open anamariaUIC opened 3 years ago

anamariaUIC commented 3 years ago

Hello,

Can you please tell me from where I can download this data: i) Gene expression data: All_Tissue_Site_Details_Analysis.combined.rpkm.gct ii) Phenotype data: phs000424.v6.pht002742.v6.p1.c1.GTEx_Subject_Phenotypes.GRU.txt iii) Sample attribute: GTEx_Data_V6_Annotations_SampleAttributesDS.txt

Is All_Tissue_Site_Details_Analysis.combined.rpkm.gct gene expression data for all tissues combined (from Gtex) and did you make that file? Or is it maybe this file: GTEx_Analysis_v6p_RNA-seq_RNA-SeQCv1.1.8_gene_rpkm.gct.gz from https://data.broadinstitute.org/snowman/ofer/GTEX/

Is Phenotype data from Gtex and requires special permission?

Is Sample attribute file this one https://data.broadinstitute.org/snowman/ofer/GTEX/GTEx_Data_V6_Annotations_SampleAttributesDS.txt

Also did you make this file genotype.v6.chr1_22.Rdata or did you downloaded it (after applying for access) and from where?

What is target ID for lymphoblastoid cell line tissue? I plan to do my analysis for that tissue instead of Whole Blood.

Does this code work with R version 4.1.0 or which other version do you recommend? Thanks Ana

egko13 commented 1 year ago

Hello, Did you find the files eventually? I am trying to run the code, but having trouble with accessing some of the files

Thanks, Eirini