Expected counts in GTEX

Question

[Pallavi]

Hi Everyone,

I wanted to ask about the GTEX transcript expected count matrix from - https://gtexportal.org/home/datasets (GTEx_Analysis_2017-06-05_v8_RSEMv1.3.0_transcript_expected_count.gct.gz)

Are these read counts just normal integer read counts or is there some normalization applied. I was interested in the gene counts value only.

Thanks!

Answer 1

[swbarnes2]

Expected counts from RSEM is fine to use. Using tximport to read in the whole rsem output and make use of the estimated gene length offsets would be slightly superior, but if you don't have that, expected counts is valid.