Question: Download data from TCGA
0
gravatar for emi.ptt
3 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 • 183 views
ADD COMMENTlink modified 3 months ago by mbk0asis220 • written 3 months ago by emi.ptt0
1
gravatar for mbk0asis
3 months ago by
mbk0asis220
Korea, Republic Of
mbk0asis220 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 3 months ago • written 3 months ago by mbk0asis220
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