How to get FASTQ files for diseased and receptive normal samples from TCGA database?

Question

[pbio]

Hi, I am completely a newbie in the field of NGS-RNAseq. But I have a set pipeline to do RNAseq analysis. But to start with my analysis I need to go with TCGA database. But I cannot find any fastq files and the normal samples for the respective data set. Please guide me how to work with TCGA database to download fastq files for specific type of cancer with the respective normal samples to do the RNA-seq analysis?

I've queried Breast invasive carcinoma [BRCA], which gave me 1094 mRNA cases. And number of NT and TN samples are listed out. but for RNAseq level 1 no data is available, for level 2 only vcf files are available and for level 3 all the outputs and analysis files are available.

Thanks in advance

Answer 1

[Sean Davis]

The Level 1 data are controlled access for ethical reasons. See that "Controlled Access Data" section on this site for details and the process.

https://tcga-data.nci.nih.gov/tcga/tcgaAccessTiers.jsp