Question: Normal Samples From ICGC
0
gravatar for David_emir
14 days ago by
David_emir310
India
David_emir310 wrote:

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.

normal_samples icgc • 66 views
ADD COMMENTlink written 14 days ago by David_emir310

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...

ADD REPLYlink written 14 days ago by Kevin Blighe37k

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.

ADD REPLYlink written 10 days ago by David_emir310

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

You can contact them at dcc-support@icgc.org

The usual program to download the data is icgc-get

ADD REPLYlink written 10 days ago by Kevin Blighe37k
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