Question: get case submitter ID for GDC miRNA quantification files
3
gravatar for murathong
16 months ago by
murathong100
China
murathong100 wrote:

I downloaded hundreds of miRNA quantifications files from GDC and wanted to analyze its association with clinical information. The problem is how to get corresponding sumitter ID (previous TCGA barcode) of each file.

This is an example: https://gdc-portal.nci.nih.gov/files/b2804bb2-70f4-471a-b6db-70c0ef457df3

I can view the case UUID (79e469c5-c18c-4c20-aaa2-8866623229d9) and view the submitter id (TCGA-BP-4343) by clicking the link. Where can I downloaded submitter id for hundreds of files?

Thanks for any hint.

mirna gdc tcga uuid • 1.4k views
ADD COMMENTlink modified 15 months ago • written 16 months ago by murathong100
3
gravatar for murathong
15 months ago by
murathong100
China
murathong100 wrote:

following the instruction on https://gdc-docs.nci.nih.gov/API/Users_Guide/Search_and_Retrieval I figured out how to download the uuid and barcode associated with each miRNA quantification file.

first determine how many files there are curl 'https://gdc-api.nci.nih.gov/files/ids?query=mirnas.quantification.txt&pretty=true'

we can see that there are 11488 files in total:

{
  "data": {
    "pagination": {
      "count": 5, 
      "sort": "", 
      "from": 1, 
      "page": 1, 
      "total": 11488, 
      "pages": 2298, 
      "size": 5
    },

then, we can retrieve all the files with:

curl 'https://gdc-api.nci.nih.gov/files/ids?query=mirnas.quantification.txt&pretty=true&size=11488&format=TSV' >submitter_ids.tsv

additional fields can be added to select columns.

ADD COMMENTlink written 15 months ago by murathong100
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