Question: Download data from TCGA
0
gravatar for emi.ptt
7 months ago by
emi.ptt0
emi.ptt0 wrote:

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 • 440 views
ADD COMMENTlink modified 3 months ago by smsinks0 • written 7 months ago by emi.ptt0
1
gravatar for mbk0asis
7 months ago by
mbk0asis240
Korea, Republic Of
mbk0asis240 wrote:
  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'.

ADD COMMENTlink modified 7 months ago • written 7 months ago by mbk0asis240
1
gravatar for TriS
3 months ago by
TriS3.1k
United States, Buffalo
TriS3.1k wrote:

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

ADD COMMENTlink modified 3 months ago • written 3 months ago by TriS3.1k
0
gravatar for smsinks
3 months ago by
smsinks0
smsinks0 wrote:
  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?

ADD COMMENTlink written 3 months ago by smsinks0
0
gravatar for smsinks
3 months ago by
smsinks0
smsinks0 wrote:

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

Cheers mate :)

ADD COMMENTlink written 3 months ago by smsinks0
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