How to download metadata for the Broad Firehose RNA-seq data?
Hello, everyone!
I just started my journey with TCGA data, and completely confused how to get the metadata for RNA-seq data.
I dowloaded rnaseqv2 RSEM normalized genes count from here.
I have count now and sample IDs, but I can't find where I can download the file with sample IDs, what is normal tissue and what is cancer (basically column_data for DeSeq2. Could you please help me with that? I can't find this in the description or tutorials.
Thank you so much for your time and help!
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mebius_band •
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You may want to get the data directly from GDC Portal/analysis center for the TCGA data: https://portal.gdc.cancer.gov/analysis_page?app=Projects
You will be able to select TCGA-BRCA project and have all data associated with the project available in a unified interface. Sounds like you don't need the sequence data which is in dbGaP and not available in the portal.
There are video tutorials available on how to use the portal: https://docs.gdc.cancer.gov/Data_Portal/Users_Guide/Video_Tutorials/