how to find sample type information from TCGA?

Question

[aichen]

After download batches of gene expression files from TCGA gdc (about 600 hundreds files), each file contains only one sample. I wanna know which file is a tumor sample, which file is a normal sample. I want to find differentially expressed genes via these genes next step. However, I don't know how to find sample type information in TCGA, anyone can help me? What I want is like this, a wiki of TCGA, because I didn't find similar tools in gdc.

I hope I can download a tab-delimited file contain these information:

study  **barcode**                   disease  disease_name                  **sample_type**  sample_type_name  analyte_type  library_type  center    center_name  platform  **filename**
TCGA   TCGA-56-7222-01A-11R-2045-07  LUSC     Lung squamous cell carcinoma  TP               01                RNA           RNA-Seq       UNC-LCCC  UNC-LCCC     ILLUMINA  UNCID_2195465.13daa1a0-a236-474e-b621-eb131be34af1.120305_UNC16-SN851_0133_AC0JB6ACXX_6_GGCTAC.tar.gz

Answer 1

[EagleEye]

TCGA-56-7222-01A-11R-2045-07

Tumor types range from 01 - 09, normal types from 10 - 19 and control samples from 20 - 29

https://wiki.nci.nih.gov/display/TCGA/TCGA+barcode?desktop=true¯oName=unmigrated-inline-wiki-markup

You can get tab-limited files for all cancer types using CgHub as manifest files, since CgHub is discontinued you can try with gdc portal,

https://gdc-portal.nci.nih.gov/search/s?filters=%7B%22op%22:%22and%22,%22content%22:%5B%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.project.program.name%22,%22value%22:%5B%22TCGA%22%5D%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.project.project_id%22,%22value%22:%5B%22TCGA-BRCA%22%5D%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.project.disease_type%22,%22value%22:%5B%22Breast%20Invasive%20Carcinoma%22%5D%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.project.primary_site%22,%22value%22:%5B%22Breast%22%5D%7D%7D%5D%7D

[aichen]

Thanks for answering me, but do you know how to get the corresponding TCGA barcode of a given file name, eg. file "UNCID_1840921.148d34df-aec2-42bf-8e36-b91a68959606.sorted_genome_alignments.bam" is belong to "TCGA-43-7657-11A-01R-2125-07"

[aichen]

I used to get tab-limited files, but I didn't find a similar filter tools in gdc

[EagleEye]

Yes GDC is bit confusing right now. I wish they will improve the documentation in future.

Select Data -> cancer program TCGA + project TCGA-XXXX ( in cases tab) -> Data format TSV ( on files tab)

Then Download Manifest

I hope this works.

Or try with GDC tool,

https://gdc-docs.nci.nih.gov/API/PDF/API_UG.pdf#page50

Manifest endpoint

[aichen]

Thanks for replying me ! But I'm sorry to say that it didn't work because I got the file like this: id filename md5 size state b99b9f44-00d2-443c-93f2-b0357491ed63 isoforms.quantification.txt a20f30bc3fe55fae1433949495884514 358879 submitted 1a657f88-2a88-4c46-b7ce-4d48c6d6ba15 isoforms.quantification.txt 3042012a718a35a59acd74bd97a1d257 410661 submitted

I found if I click download, choose "biospeciman" or "File metadata" , I can get these information including "TCGA barcode", "file name" etc. , but the format is ".json" :(

Thank you all the same!

[EagleEye]

Thats great. You can try converting Json to csv ot tsv using some tools like this,

http://www.convertcsv.com/json-to-csv.htm

I hope it works.

[aichen]

Great! Thanks a lot :)

[Mike]

Broad-GDAC could be alternative way to download TCGA data

https://gdac.broadinstitute.org/

[aichen]

Thanks, it can export pdf.

[Chun-Jie Liu]

Hi did you solve the problem? Converting GDC filename to TCGA barcode to find tumor or normal sample information

[Chun-Jie Liu]

Did you solve the problem? I met same problem to convert filename TCGA barcode to find tumor normal information.