Question: Download data from TCGA
0
gravatar for emi.ptt
5 weeks 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 • 121 views
ADD COMMENTlink modified 5 weeks ago by mbk0asis200 • written 5 weeks ago by emi.ptt0
1
gravatar for mbk0asis
5 weeks ago by
mbk0asis200
Korea, Republic Of
mbk0asis200 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 5 weeks ago • written 5 weeks ago by mbk0asis200
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