Question: Getting raw FASTQ file from GDC/TCGA database
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gravatar for bharata1803
9 months ago by
bharata1803440
Japan
bharata1803440 wrote:

Hello,

I just want to know whether we can obtain raw data from GDC/TCGA database. I heard they require you to submit some request but I don't know how to do it. I am a student so my credentials is very limited. Maybe I can ask my Professor to submit it if needed. Also does it takes long time for the request submission process? Thank you.

rna-seq next-gen • 569 views
ADD COMMENTlink modified 9 months ago by Biostar ♦♦ 20 • written 9 months ago by bharata1803440

The guidelines for accessing restricted data are here. Typically a PI or professor submits the request. Be aware the process of revision can take some weeks. What exactly do you need, maybe there are other ways to help you out.

ADD REPLYlink written 9 months ago by ATpoint26k

well, I need the raw data because I want to use transcript level gene expression for my method. Unfortunately, GDC only has gene level expression result. So, I think having raw data myself, I could get the transcript level expression by myself.

Currently I use data from NCBI GEO because there are many dataset that provide raw FASTQ but the samples, sometimes, are small in number compare to TCGA dataset and NCBI GEO are not really easy to search. I want something like TCGA in terms of cancer data. It has been categorized based on tissue or cancer type so it is easy to get. I can also get normal and cancer samples from TCGA. Experiment data published in NCBI GEO sometimes not cancer vs normal.

ADD REPLYlink modified 9 months ago • written 9 months ago by bharata1803440
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