Normal Samples From ICGC

Question

[David_emir]

Hi All,

I am looking for downloading Only Normal Samples (RNA-seq) Raw counts for Pancreatic Adenocarcinoma from International Cancer Genome Consortium (ICGC), But, I am ending up downloading only Tumor samples file, can you guys let me know how to get Normal samples Raw counts from ICGC?

Regards

Dave.

Answer 1

[Kevin Blighe]

Hey Dave, can you clarify from where, exactly, you are downloading the data? I can easily configure a search for normal tissue from pancreatic cancer patients at the ICGC Data Portal: https://dcc.icgc.org/repositories?files=%7B%22from%22:1,%22si...

[David_emir]

Hi Kevin,

I am downloading the data from ICGC-Pancreatic Cancer. The Sequencing-based Gene Expression data file contains 91 samples. whereas the Clinical Specimen file says it also contains Solid normal samples which I am not able to download. For Example Specimen Ids such as "SP108126, SP108104, SP108107, SP108090, SP108052, SP108072, SP108069" are missing and all 91 samples are from Tumors. It would be great if you let me know how to download the normal samples.

[Kevin Blighe]

I believe DACO controls access to that data: https://icgc.org/index.php?q=daco

You can contact them at [e-mail]

The usual program to download the data is icgc-get