Question: GTEx v10 smallRNA expression read counts

Help
1

Hi,

The improvement from GTEx v8 is really impressive and I believe a lot of people will benefit from it. I have a question regarding the data for small RNA-seq (this one: GTEx_Analysis_v10_smallRNA_gene_reads.txt.gz). The data doesn’t seem to be a raw count (I assume) and there are some negative values as well in the table. What would that be, if some normalization was performed?

Thanks!

Best,
Farhad

2

Hello @farzamani,

Thank you for your question!

I opened a ticket with the GTEx portal to ask for some clarification here. Will get back to you as soon as we hear from them.

Javier

3

Hi Javier, thanks for your help!

4

Hello, I just wanted to ask if there’s been any update on this topic? I was having the same question as Farhad would be really thankful for any explanation about how to interpret the numbers in the smallRNA reads file. Thanks in advance.

Ignas

5

Hi @Ignas,

If you haven’t checked in the portal, they have now updated the smallRNAseq data, including the metadata and annotation.

Best,
Farhad

6

Thank you @farzamani for the update!

Attaching the link to the documentation:

Best,