Question: TCGA BRCA Solid Tissue Normal Filter
0
gravatar for tweiskittel94
13 months ago by
tweiskittel940 wrote:

I am a new TCGA user and need to download all the solid tissue normal transcriptome files from the TCGA BRCA project. I have been able to find all the solid tissue normal samples (there seems to be about 70) through a really round about way. What is the easiest way to find all the TCGA BRCA Solid Tissue normal files and download them? I have tried a case filter, but it does not recognize solid tissue normal as a valid filter. Thanks!

solid tissue normal tcga • 960 views
ADD COMMENTlink modified 13 months ago by shoujun.gu370 • written 13 months ago by tweiskittel940
2
gravatar for Kevin Blighe
13 months ago by
Kevin Blighe44k
Kevin Blighe44k wrote:

Easiest way to find out which files are the normal tissues is:

  1. go to the GDC Legacy and pick the samples that you want from the checkboxes (at left). Here is a selection for BRCA RNA-seq gene-level counts: https://portal.gdc.cancer.gov/legacy-archive/search/f?filters=%7B%2...
  2. Download the manifest via the Download Manifest button
  3. In R, look up the TCGA barcode for each file ID (UUIDs) in the manifest (first column) using this function posted by a colleague: C: Sample names for TCGA data from GDC-legacy archive
  4. Distinguish tumour from normal based on the barcode - see A: Meaning letters in TCGA sample barcode field

There may be many other ways to do this, but this one is relatively quick (relative to other roundabout was of doing it).

Kevin

ADD COMMENTlink modified 13 months ago • written 13 months ago by Kevin Blighe44k
2
gravatar for shoujun.gu
13 months ago by
shoujun.gu370
Rockville/MD
shoujun.gu370 wrote:

GDC provides the sample sheet file, in which there is the information about whether an sample is normal or tumor. You could filter the samples by writing a python or R script.

ADD COMMENTlink written 13 months ago by shoujun.gu370

Please be more specific. Where can one obtain the sample sheet? Does it show, for each file, whether it relates to a tumour or normal?

ADD REPLYlink written 13 months ago by Kevin Blighe44k
  1. add your files to your cart
  2. go to your cart page, there is a 'sample sheet' download button. download that tsv file
  3. the sample sheet tsv file contains columns: File ID File Name Data Category Data Type Project ID Case ID Sample ID Sample Type
  4. match your sample file name with the 'Sample Type'
ADD REPLYlink written 13 months ago by shoujun.gu370
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