How to understand the data and the sample for BS-seq data from TCGA

Question

[Shicheng Guo]

I notice there are BS-seq data in TCGA Project, however, there is no samplesheet to explain the relationship between BS-seq files in GDC with sample ID.

How to deal with this problem? Such as

> ResultCount_MERGING_1_NIC1254A17.hg19_rCRSchrm.fa.realign.mdups.recal.cpg.filtered.sort.CG.6plus2.fixed.bed

Which sample it is?

Thanks.

[Devon Ryan]

The image you tried to link to seems to be a "riff" file, which I'm not sure many people can open.

[Shicheng Guo]

Hi Devon, No, these BS-seq files were opened several days ago, before that, they are controlled private data. You can check these BedDetail format data with the following link: https://gdc-portal.nci.nih.gov/legacy-archive/search/f?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:%22files.data_category%22,%22value%22:%5B%22DNA%20methylation%22%5D%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_type%22,%22value%22:%5B%22Bisulfite%20sequence%20alignment%22,%22Methylation%20percentage%22%5D%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.access%22,%22value%22:%5B%22open%22%5D%7D%7D%5D%7D

Answer 1

[Shicheng Guo]

Okay. I received the answer from GDC with API to get sample name:

curl "https://gdc-api.nci.nih.gov/legacy/files/4a8ffe0d-d7e6-4712-ad04-472955c84c77?fields=cases.samples.portions.analytes.aliquots.submitter_id,cases.samples.sample_type&format=tsv"
curl "https://gdc-api.nci.nih.gov/legacy/files/087ec4fb-a621-4fcf-8276-1c74782bcc2c?fields=cases.samples.portions.analytes.aliquots.submitter_id,cases.samples.sample_type&format=tsv"

Answer 2

[nwon]

sampleID's are now replaced with UUIDs, the Case UUID is the one you would be interested in, from there and from a GDC manifest file, it is possible to find the TCGA-XXXX sample ID.

UUID to Sample Barcodes in R

GDC Wiki on UUIDs and TCGA Sample Barcodes