Hello, This might be a silly question but I couldn't find a tag to select triple negative breast cancer samples in GDC. I've tried downloading metadata of RNA-seq files and also clinical metadata but couldn't find a tag. I've also downloaded a single clinical file and tried searching for a tag but no luck. I've even searched for any posts for this problem but couldn't find any. Is there anyway I can download triple negative data?
Normally, I try to download data using GDC tool. Is there any other which might help me downloading TCGA data specific to triple negative breast cancer data?
Please help me with this. Thank in advance!
Thank you for the solution. I've downloaded the clinical file and it's been difficult to map the IDs from clinical to that of expression matrix. Fortunately, I know how to code and mapped them back. Also, the clinical file I've obtained doesn't have any information regarding to control/normal samples.
Yes, determining tumour versus normal can be difficult. You should search for a particular file name, UUID, or something else using the Data Portal and then infeer tumour or normal via the TCGA barcode.
In the clinical data that you've downloaded, most likely each record (row) relates to a patient, which itself relates to multiple tumour biopsies and [most likely] a normal.
It is cumbersome working with this data - I know
Not sure if you are still watching this thread, mtkk94, but I have edited the final part of my answer with new information on a very rapid way to map UUIDs to TCGA Barcodes, which can then be used to distinguish tumor from normal.
saw this post mentioned in a DNANexus tutorial