Processing GTEx RNA-Seq data using the TCGA bioinformatic pipeline

Question

[smsinks]

I would like to compare TCGA RNA-Seq data to that of normal tissue expression from the GTEx project. However, the FPKM values reported by the TCGA higher than those reported by the GTEx project for the same normal tissue. I have traced this to the different bioinformatics pipelines used to the two project. I now have the CUSTOM SCRIPTS that were used by the TCGA to obtain the upper quantile normalised FPKM values. However, I am not sure which GTEx data to process using these scripts. Should I use the "Gene read counts" or "Transcript read counts"? Refer to the screenshot of the GTEx data portal given in the link below. Also, I have contact GTEx twice but I have not received a response from them.

Answer 1

[igor]

You should consider using RNAseqDB where they analyzed TCGA and GTEx data together (and even applied batch correction): https://github.com/mskcc/RNAseqDB

[smsinks]

This is exactly what I was looking for. Cheers!