GTEX RNA Seq. Pipeline
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Entering edit mode
17 months ago
Bine ▴ 40

Dear all,

This is my first post here and I am hoping you can help me.

I am currently doing a RNA Seq. Analysis of our inhouse data and for this I followed the GTex Pipeline (because later on I want to compare our data to the GTex Data).

In order to continue with a Differential Expression Analysis I want to use DeSeq or edgeR but both require raw reads of genes. The table I have been looking at called "genes" only gives length, effective length, expected_count, TPM and RPKM. TPM and RPKM are already normalised counts but I need the raw counts. Do you know which output of the GTEX RNASeq Pipeline shows the raw counts per sample?

I am looking forward to hear from you.

Thank you very much :)

Bine

RNA-Seq Raw_data GTex • 489 views
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