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Welcome to the Broad Institute Genome Data Analysis Center (GDAC) online help forum. Please see our website for more information, including how to submit bug reports directly to our issue tracking system. The Broad GDAC endeavors to answer questions posted to this list as quickly as possible, often within 1 to 24 hours; however, due to the formal end of TCGA in July of 2016--and our reduction in staffing and focus on emerging projects--you may experience longer response times.

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Mariano S. Viapiano2

6/12/24

FireBrowse webpage no longer available.

Hello David, Thanks so much for your quick response on this. My lab and I truly appreciate all the

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FireBrowse webpage no longer available.

Hello David, Thanks so much for your quick response on this. My lab and I truly appreciate all the

6/12/24

Broad Institute GDAC

5/28/24

Re: website broken?

All I can find is https://www.cancer.gov/ccg/research/genome-sequencing/tcga/using-tcga-data, and it

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Re: website broken?

All I can find is https://www.cancer.gov/ccg/research/genome-sequencing/tcga/using-tcga-data, and it

5/28/24

'Kirkconnell, Brett' via gdac2

8/29/23

Hi Brett, Unfortunately our confluence site got moved, and it does not match up with our old one.

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Hi Brett, Unfortunately our confluence site got moved, and it does not match up with our old one.

8/29/23

Broad Institute GDAC2

6/7/23

Re: Error connecting to port 80

To Whom it may Concern, I'm having trouble connecting to your website to download data on breast

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Re: Error connecting to port 80

To Whom it may Concern, I'm having trouble connecting to your website to download data on breast

6/7/23

Aswathymary Paul

3/17/23

Access to hg38 data

Hello, I was looking for mRNA expression of transcripts AR. I could only find 5 transcripts'

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Access to hg38 data

Hello, I was looking for mRNA expression of transcripts AR. I could only find 5 transcripts'

3/17/23

Broad Institute GDAC

12/13/22

Re: GDAC Firehose broken?

Hi Maciej, The only tools that we support are fbget and firehose_get. All R tools were developed by

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Re: GDAC Firehose broken?

Hi Maciej, The only tools that we support are fbget and firehose_get. All R tools were developed by

12/13/22

Gordon Saksena, David Heiman2

3/23/22

Re: Migrating RHEL6 hosts - - Final Reminder

It should be okay to migrate most of these to RHEL7 - preferably during the next quarterly

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Re: Migrating RHEL6 hosts - - Final Reminder

It should be okay to migrate most of these to RHEL7 - preferably during the next quarterly

3/23/22

10/9/20

Different samples with TCGA Illumina 450K methylationn data between Firebrowse and GDC

Hello, I was comparing the TCGA samples that are available from GDC and Firebrowse and that have

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Different samples with TCGA Illumina 450K methylationn data between Firebrowse and GDC

Hello, I was comparing the TCGA samples that are available from GDC and Firebrowse and that have

10/9/20

'Jatin Khaimani' via gdac2

5/14/20

URGENT HELP needed for citing Broad Institute's work

Hi Jatin, Our confluence site got moved, and many of the redirects broke. The correct link is here:

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URGENT HELP needed for citing Broad Institute's work

Hi Jatin, Our confluence site got moved, and many of the redirects broke. The correct link is here:

5/14/20

Sarah Mason, Gdac-users2

4/29/20

Hi Sarah, Can you please be more specific? How are you acquiring the data - the web API, a command-

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Hi Sarah, Can you please be more specific? How are you acquiring the data - the web API, a command-

4/29/20

Kaoru Sakabe, Gdac-users3

4/6/20

Site keeps timing out

Hi David, I'm trying to get more information regarding the dataset found at this URL: https://doi

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Site keeps timing out

Hi David, I'm trying to get more information regarding the dataset found at this URL: https://doi

4/6/20

木暮　泰寛

3/13/20

CoMut plot in FireBrowse using GISTIC2 result

Hello, I am trying to figure out how to create the CoMut plot like this. http://firebrowse.org/iCoMut

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CoMut plot in FireBrowse using GISTIC2 result

Hello, I am trying to figure out how to create the CoMut plot like this. http://firebrowse.org/iCoMut

3/13/20

Gorostiola Gonzalez, M.

2/12/20

Tumor microenvironment in TCGA data

Dear sir/madam, My name is Marina Gorostiola González. I am a PhD candidate in the group of Gerard

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Tumor microenvironment in TCGA data

Dear sir/madam, My name is Marina Gorostiola González. I am a PhD candidate in the group of Gerard

2/12/20

12/12/19

question about brain metastatic lesions

Hello and thanks very much for curating Firebrowse, I'm a medical resident datamining FireBrowse

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question about brain metastatic lesions

Hello and thanks very much for curating Firebrowse, I'm a medical resident datamining FireBrowse

12/12/19

Mariano Viapiano, Broad Institute GDAC3

11/6/19

Server confluence.broadinstitute.org is down

Thank you David, I appreciate it! (it has been a while since last time we used it!) Best regards,

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Server confluence.broadinstitute.org is down

Thank you David, I appreciate it! (it has been a while since last time we used it!) Best regards,

11/6/19

Lisa George, Gdac-users3

10/28/19

query regarding the gene-level CNV breast cancer dataset from the TCGA data hub

Hi Lisa, We provide the TCGA data we generated via our data portal, firebrowse.org. Please take the

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query regarding the gene-level CNV breast cancer dataset from the TCGA data hub

Hi Lisa, We provide the TCGA data we generated via our data portal, firebrowse.org. Please take the

10/28/19

geral...@web.de

10/22/19

Firebrowse.org - REST API

Dear Sir or Madam, for the URL http://firebrowse.org:8000/api/v1/Samples/mRNASeq?format=tsv&gene=

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Firebrowse.org - REST API

Dear Sir or Madam, for the URL http://firebrowse.org:8000/api/v1/Samples/mRNASeq?format=tsv&gene=

10/22/19

Sindre Lee-Ødegård

10/5/19

Available raw data?

Dear all, I am very interested in a CpG site named cg00859178. I found that methylation of cg00859178

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Available raw data?

Dear all, I am very interested in a CpG site named cg00859178. I found that methylation of cg00859178

10/5/19

9/27/19

Firehose Broad GDAC website unavailable

To whom it may concern, I am exploring the TCGA data on your website and found I can not open the “

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Firehose Broad GDAC website unavailable

To whom it may concern, I am exploring the TCGA data on your website and found I can not open the “

9/27/19

Eskil Eskilsson

9/27/19

Firehose TCGA Data Usage Policy access

GDAC Data Manager: I cannot view the Firehose TCGA Data Usage Policy via the link at the bottom of

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Firehose TCGA Data Usage Policy access

GDAC Data Manager: I cannot view the Firehose TCGA Data Usage Policy via the link at the bottom of

9/27/19

9/20/19

Replication of the TCGA PARADIGM analysis

Dear TCGA GDAC Team, We are trying to reproduce the PARADIGM analysis according to what was reported

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Replication of the TCGA PARADIGM analysis

Dear TCGA GDAC Team, We are trying to reproduce the PARADIGM analysis according to what was reported

9/20/19

9/16/19

GenomeSpace sunset

As a follow-up, please contact us if you are interested in continuing to have connectivity for

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GenomeSpace sunset

As a follow-up, please contact us if you are interested in continuing to have connectivity for

9/16/19

Marcel Ramos, Gad Getz2

9/14/19

Dear Marcel, You have permission to use the logo with a citation to the Broad Institute's Genome

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Dear Marcel, You have permission to use the logo with a citation to the Broad Institute's Genome

9/14/19

9/13/19

Question About Types of Analysis

I am trying to better understand how to use FireBrowse. From what I can see, I can perform analysis

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Question About Types of Analysis

I am trying to better understand how to use FireBrowse. From what I can see, I can perform analysis

9/13/19

9/11/19

TCGA data access policy

Dear GDAC, The url at the bottom of the gdac firehose [1] for TCGA data sharing policies [2] is

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TCGA data access policy

Dear GDAC, The url at the bottom of the gdac firehose [1] for TCGA data sharing policies [2] is

9/11/19

a.bha...@uliege.be

9/2/19

Regarding Most updated release in TCGA firebrowse

Dear Sir/Maam Greeting!! I am working on PDAC multi-omics data analysis and interpretation. We have

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Regarding Most updated release in TCGA firebrowse

Dear Sir/Maam Greeting!! I am working on PDAC multi-omics data analysis and interpretation. We have

9/2/19

Bense, RD (onco), Gdac-users2

8/27/19

Preprocessed methylation data Firehose

Dear Rico, Please see https://broadinstitute.atlassian.net/wiki/spaces/GDAC/pages/844333886/

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Preprocessed methylation data Firehose

Dear Rico, Please see https://broadinstitute.atlassian.net/wiki/spaces/GDAC/pages/844333886/

8/27/19

'Sinkoe, Andrew (NIH/NCI) [F]' via gdac

8/23/19

bioinformatics pipeline for TCGA DLBC

Hi, I'm having a hard time finding information about the specific bioinformatics tools that were

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bioinformatics pipeline for TCGA DLBC

Hi, I'm having a hard time finding information about the specific bioinformatics tools that were

8/23/19

sk...@broadinstitute.org

8/12/19

Invitation: ACB Interview Talk: Yao Tong @ Wed Aug 14, 2019 10:30am - 10:50am (EDT) (gdac)

You have been invited to the following event. more details » ACB Interview Talk: Yao Tong When Wed

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Invitation: ACB Interview Talk: Yao Tong @ Wed Aug 14, 2019 10:30am - 10:50am (EDT) (gdac)

You have been invited to the following event. more details » ACB Interview Talk: Yao Tong When Wed

8/12/19

Yihong Jennifer Tan

8/6/19

Enquiry on LAML microRNA data

Hello, I am interested in downloading the microRNA-seq data for Lymphoid Neoplasm Diffuse Large B-

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Enquiry on LAML microRNA data

Hello, I am interested in downloading the microRNA-seq data for Lymphoid Neoplasm Diffuse Large B-

8/6/19

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