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Old 12-28-2015, 11:57 AM   #1
fk566938
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Question TCGA RNAseq BAM Files

Hi

My PI is interested in acquiring BAM files of RNAseq of breast cancer/cancer tumor/cell lines. I know TCGA may have them, how can we proceed to access this data?
Also the Broad Institute's "IGV" application seems to have an accessible TCGA Server, however the data does not seem to be RNAseq. Does anyone know how to utilize the TCGA server on IGV?
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Old 12-29-2015, 09:10 AM   #2
m_two
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Before obtaining and reprocessing the sequence data on your own I would review the freely available and open access processed data.

* https://wiki.nci.nih.gov/display/TCGA/RNASeq+Version+2 - http://www.webcitation.org/6e8quhoOJ

* Firehose
** Firebrowse Firehose Browser http://firebrowse.org
** Open access portal http://gdac.broadinstitute.org/runs/...__latest/data/
** Command line tools include fbget and firehose_get

If the processed data do not meet your needs you need to apply for permission access to the BAMs through dbGaP.

The dbGaP accession for TCGA data is phs000178
http://www.ncbi.nlm.nih.gov/projects...y_id=phs000178

====dbGaP access in a Nutshell====

The individual level genotype and phenotype data are available through the dbGaP Authorized Access System (http://dbgap.ncbi.nlm.nih.gov/aa/wga...in=&page=login).

Adding someone is easy once a PI has obtained an account.
The PI can login, then using the third tab initiate a search for ERA users, find the user's account ID and add the user access.

Collaborators/PIs outside the institution must apply for access separately.


====dbGaP access details====


You will need an NIH eRA login account and be identified by your institution as a primary investigator to log into the system. The eRA is not operated by NCBI. Their account registration system is online at https://commons.era.nih.gov/commons/...structions.jsp .

Data request procedures are summarized in the document https://dbgap.ncbi.nlm.nih.gov/aa/db...st_process.pdf .

In addition, there is a dbGaP FAQ archive that may have instructions that you need. Here is a link to the section of the archive that shows you how to start the process. http://www.ncbi.nlm.nih.gov/bookshel...part=DArequest .

Please reply to [email protected] if you have further questions after reviewing these items.

Regarding data security procedures, review http://www.ncbi.nlm.nih.gov/projects...procedures.pdf


Adding Data Downloaders to Approved Requests:

Once you are an approved user, you may designate members of your group to download data using your credentials.
Log into dbGaP Authorized Access system: https://dbgap.ncbi.nlm.nih.gov/aa/wga.cgi?page=login ; there may be a lag of 24-48 hours between creating the eRA Commons account and when that information propagates to the NIH servers.
Click on the ‘Downloaders’ (third) tab
Search for the user you wish to designate as a data downloader
The user must
1) be in your institution
2) have an eRA Commons account (this can be created by the Signing Official or Research Administrator)
3) have successfully logged into the dbGaP Authorized Access system at least once
Select the user and verify his/her information
Select the projects for the user to have access to or select all
When finished, click ‘Set downloader’
The downloader will receive an email from NCI CBIIT to set up their NCI username and password. If not, have the downloader email CBIIT directly: [email protected].
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Old 12-29-2015, 09:27 AM   #3
fk566938
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Thank you for all the information m_two I will see if I can utilize this accordingly
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