Hello,

 

I'm running DESeq and EdgeR on RNA-Seq data that was already processed with
RSEM (downloaded from TCGA web site).

Since these methods require the raw read counts I'm using the raw_count
column of the RSEM output but I'm not sure this is the right thing to do (is
it the actual raw count required ?)

 

Here's an example file for the RSEM output file downloaded from TCGA:

 


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


TCGA-A1-A0SB-01A-11R-A144-07

?|100134869

31.95

8.40876E-07

uc002bgz.2,uc002bic.2


TCGA-A1-A0SB-01A-11R-A144-07

?|10357

258.35

2.16969E-05

uc010zzl.1


TCGA-A1-A0SB-01A-11R-A144-07

?|10431

1459

5.53441E-05

uc001jiu.2,uc010qhg.1

 

 

Many thanks,

Dvir


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