Question: TCGA raw data (Level 1)
0
gravatar for H.Hasani
2.3 years ago by
H.Hasani970
Freiburg, Germany
H.Hasani970 wrote:

Dear all,

now that TCGA is closed, I was wondering if it is possible to obtain level 1 files. Those files were typically available via controled access. I tried firehose but I got only Level 3. I'm looking for SNP6 data (CEL files) and RNA (ideally fastq). In case not, could you please recommend an alternative way?

thank you very much

snp rna-seq copy number • 1.9k views
ADD COMMENTlink written 2.3 years ago by H.Hasani970
1

TCGA Data has moved to Genomic Data Commons (https://gdc-portal.nci.nih.gov/). Unfortunately SSL cert on that site has expired and will generate errors in browsers (I just sent a ticket in to them for this, see their response below). You can apply for access to controlled data there.

GDC Portal URL has changed to: https://portal.gdc.cancer.gov/

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by genomax90k
1

As per GenoMax, data has been moved but it is most certainly still available. I've been downloading Level 1 data for the past week. You will need to request access via dbGaP, with information being provided through the link that GenoMax has provided.

Once you obtain access, you will have an eRA Common account created for you. You can use this to log-in at the GDC Data Portal. Once logged in, you can download a 'token' file. This token file can then be used in conjunction with a file manifest for the purposes of downloading any Level 1, 2, or 3 files via the GDC Data Transfer tool.

ADD REPLYlink written 2.3 years ago by Kevin Blighe65k
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