Question: How to get FASTQ files for diseased and receptive normal samples from TCGA database?
2
gravatar for pbio
4.2 years ago by
pbio120
United States
pbio120 wrote:

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..

rna-seq tcga • 2.5k views
ADD COMMENTlink modified 4.2 years ago by Sean Davis25k • written 4.2 years ago by pbio120
3
gravatar for Sean Davis
4.2 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

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

ADD COMMENTlink written 4.2 years ago by Sean Davis25k
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