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

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?

icgc rna-seq pcawg
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written by Sonia • Sonia

1 answer

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.

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written by ATpoint ATpoint

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.

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written by Hamid Ghaedi Hamid Ghaedi

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
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written by GenoMax GenoMax

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

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written by Sonia • Sonia

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