Re: [GDAC-users] Synovail Sarcoma TCGA Reads

Subject:   Re: [GDAC-users] Synovail Sarcoma TCGA Reads (more for this subject)
From:   Michael Noble <> (more from this sender)
Date:   Oct 26, 2015 15:50

Hello John,
Yes, it’s possible.  But it requires some legwork beyond our walls:  because BAM-level (or fastq) data is available from CGHUb, and requires protected-data access credentials (as described therein).  We don’t serve that data in our GDAC.
On Oct 26, 2015, at 3:44 PM, John L Pulice <> wrote:
> Hi GDAC,
> I am an associate computational biologist in the Kadoch Lab. The GDAC has ten synovial sarcoma samples available for analysis. I am hoping to find out what is needed to get the fastq files for those ten samples, so that I can analyze them alongside the other tumor sample data and cell line mRNA-seq data I have. Is that possible?
> Please let me know at your earliest convenience, and I can also supply the IDs for the samples if requested.
> Best,
> John
> --  
> John Pulice
> Associate Computational Biologist I, The Broad Institute of MIT and Harvard
> Bioinformatics Analyst I, Dana-Farber Cancer Institute
> Kadoch Lab, Department of Pediatric Oncology, Harvard Medical School
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