Question: Normal Samples From ICGC
0
gravatar for David_emir
20 months ago by
David_emir370
India
David_emir370 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 • 514 views
ADD COMMENTlink written 20 months ago by David_emir370
1
gravatar for Kevin Blighe
20 months ago by
Kevin Blighe66k
Kevin Blighe66k wrote:

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 COMMENTlink written 20 months ago by Kevin Blighe66k

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 20 months ago by David_emir370

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 20 months ago by Kevin Blighe66k
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