Download data from TCGA
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Entering edit mode
5.5 years ago
emi.ptt ▴ 30

Hi everyone,

I am not able to download mRNA data (e.g from RNAseq) from the TCGA. All the tutorials I've watched explain how download data with the OLD interface of the web page. How can I get these data with the NEW interface?

I also have another question. How can I see the presence or not of control samples in a study? Thanks!!

RNA-Seq • 13k views
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5.5 years ago
mbk0asis ▴ 660
  1. Go to GDC data portal

  2. Click 'Data'

  3. Select types of cancer and files (RNA-seq in your case)

  4. Click 'Download Manifest' and save the manifest file.

  5. Install 'GDC data transfer tool (gdc-client)'.

  6. Go to the directory containing the manifest file.

  7. In terminal (command line), type "gdc-client download -m MANIFEST_YOU_DOWNLOADED".

Files you chose will be downloaded in the current directory.

For the presence of control samples, google 'TCGA barcode'.

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Entering edit mode
5.2 years ago
TriS ★ 4.6k

easiest way:

  1. go to cBioportal
  2. click on the tumor type you want
  3. on the right side click on "summary"
  4. on the top of the page you have "download data"

..there you go

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Entering edit mode
5.2 years ago
smsinks ▴ 20
  1. Install 'GDC data transfer tool (gdc-client)'.

How is that done on MAC OSX Sierra? I ask because I have failed!

Is it via terminal or the simple double click?

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5.2 years ago
smsinks ▴ 20

Now, this is data access with no fuss. Even a toddler can do it!!!

Cheers mate :)

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