TCGA raw data (Level 1)
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
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
How to generate .AED files from .CEL files using Linux (Affymetrix CytoScan HT-CMA 96F)
written by genetixs •
-
TCGA gene models and exon/isoform level expression data
written by dolevrahat •
-
TCGA CNV data - immensely different results depending on data source
written by JJ
-
How to get AF in TCGA MutSigNozzleReport2CV Level_4
written by H.Hasani
-
TCGA data on cloud
written by oriolebaltimore
-
Tutorial: use firehose_get to download TCGA data
written by jmzeng1314
-
RNA-Seq raw fastq files from TCGA
written by oriolebaltimore
-
TCGA MAF files after migration to GDC
written by nilus1432 •
-
Consolidated MAF file for all cancers in TCGA
written by somy.ork •
-
Broad Firehose mRNA z-scores
written by dirigible2012
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/
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.