Question: Download all DNA mutations from TCGA
0
gravatar for ceruleanivy
4.2 years ago by
ceruleanivy30
ceruleanivy30 wrote:

I would like to download all the available TCGA data on mutations for colon adenocarcinoma, including every sample that was tested under this multi-institutional endeavor, but I cannot figure out how to find the desired information. By visiting the 'searchForTCGAData' page and selecting Data Catgegory: DNA mutation and Disease: COAD I get 384 different results. Do these files correspond to different patients/samples ?

ADD COMMENTlink modified 4.2 years ago by igor11k • written 4.2 years ago by ceruleanivy30

I think you can download all TCGA vcf files and parse them by yourself.

ADD REPLYlink modified 4.2 years ago • written 4.2 years ago by chen2.1k
4
gravatar for igor
4.2 years ago by
igor11k
United States
igor11k wrote:

I personally find Broad GDAC Firehose to be the easiest way to access TCGA data, especially if you want it combined: http://gdac.broadinstitute.org/runs/stddata__latest/

Update: UCSC Xena seems to be even better organized and contains more recent data: https://xenabrowser.net/datapages/

ADD COMMENTlink modified 22 months ago • written 4.2 years ago by igor11k
1
gravatar for Chris Miller
4.2 years ago by
Chris Miller21k
Washington University in St. Louis, MO
Chris Miller21k wrote:

You can download the somatic variants in MAF format here: https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/coad/gsc/hgsc.bcm.edu/illuminaga_dnaseq/mutations/hgsc.bcm.edu_COAD.IlluminaGA_DNASeq.Level_2.1.5.0/hgsc.bcm.edu_COAD.IlluminaGA_DNASeq.1.somatic.maf

ADD COMMENTlink written 4.2 years ago by Chris Miller21k
1

Looks like this URL is no longer working

ADD REPLYlink written 22 months ago by steve2.6k

try https://portal.gdc.cancer.gov/repository

ADD REPLYlink written 15 months ago by glocke01170

Thanks! May I ask how did you search in order to find the file above ? By using File Search as a method -->DNA mutation, COAD, Open Access I get two files other than descriptions rather than one.

ADD REPLYlink written 4.2 years ago by ceruleanivy30

I usually go straight to the data directories (i.e. https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/coad/) and click through from there until I get the file I need.

ADD REPLYlink written 4.2 years ago by Chris Miller21k
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