How can I download the PCAWG (ICGC/TCGA) raw counts data?

Question

[Sonia]

I want to download the raw counts (not normalized) of PCAWG transcriptome data, but the counts file which I downloaded from ICGC Data Releases seems doesn't have the raw counts.

Would you mind helping me how to find and download the PCAWG raw counts data?

Answer 1

[ATpoint]

The bioconductor package recount provides raw counts for TCGA, GTEx and SRA samples:

https://bioconductor.org/packages/release/bioc/html/recount.html

For TCGA metadata you can check:

BiocManager::install("recount")
library(recount)
tcga <- recount::all_metadata("tcga")

... and from there select what you need.

[Hamid Ghaedi]

And what about ICGC data? I couldn't find a function from recount for fetching data from ICGC. There is a count file here. However, the name denotes that to be a count( raw count?) but it seems the expression value there is float instead of being an integer.

[GenoMax]

Check: https://dcc.icgc.org/releases/current/Projects

Open-access analyzed data (if available for a project will have following names) :

• exp_array.[ICGC project code].tsv.gz: gene expression measured at the transcriptional level (mRNA) using array-based platforms
• exp_seq.[ICGC project code].tsv.gz: gene expression measured at the transcriptional level (mRNA) using sequencing-based platforms
• mirna_array.[ICGC project code].tsv.gz: array-based microRNA data
• mirna_seq.[ICGC project code].tsv.gz: sequencing-based microRNA data

[Sonia]

Exactly, also the naming of the columns is confusing and I can not discriminate between normal and tumor samples.