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Old 03-19-2013, 04:25 AM   #1
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Location: Israel

Join Date: Mar 2013
Posts: 1
Default Getting raw counts needed for Deseq/EdgeR from TCGA RSEM files


I wish to run DE analysis using DESeq or EdgeR on RNA-seq data downloaded from TCGA. I would like to use the Level 3 RNA-Seq data, which is already processed using RSEM.

I wonder if I can use the column named "raw counts" in the RSEM un-normalized output as the raw read counts needed for the input for DESeq and EdgeR.

For example, the column marked in bold in the file :


barcode gene_id raw_count scaled_estimate transcript_id
TCGA-A1-A0SB-01A-11R-A144-07 ?|100130426 0 0 uc011lsn.1
TCGA-A1-A0SB-01A-11R-A144-07 ?|100133144 34.05 1.23812E-06 uc010unu.1,uc010uoa.1

Thanks !
D. N.
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