I want to download and analyze the mutation data of TCGA. I find that the mutation data is controlled on original download source (https://portal.gdc.cancer.gov/repository). I search on net and find another source to download the data (http://gdac.broadinstitute.org/runs/stddata__2016_01_28/). This source are from a thread (https://www.biostars.org/p/189418/).
Taking BRCA as example, this is data related to mutation “gdac.broadinstitute.org_BRCA.Mutation_Packager_Calls.Level_3.2016012800.0.0.tar.gz”. I download and unzip it. There are 982 files and one file for one sample.
I find that there are no more than 100 genes with mutations in each file. Why are there so few mutations in each sample?
Where can I download a relative comprehensive mutation dataset of TCGA?
1 answer
GDC
At the Genomic Data Commons (GDC), the open access mutation data is available as Mutation Annotation Format (MAF). Here is a search configured for breast cancer (BRCA): https://portal.gdc.cancer.gov/repository?facetTab=cases&f...
Broad Institute
At the Broad Institute, there are many more files listed that contain mutation data. You happened to download just the first in the listing (alphabetically).
Xena
As per Igor in the other thread, the Xena Browser data appears to be quite neatly arranged. Take a look at GDC TCGA Breast Cancer (BRCA) (18 datasets) at https://xenabrowser.net/datapages/
Kevin
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Thanks again, Kevin I realized that I made a mistake. Unlike the expression and methylation data, the separate mutation data are controlled but the merged MAF files are open.
Hi tujuchuanli ,
This reply is better suited as a comment on Kevin's answer. Could you make the appropriate change please? That would involve the following steps:
Select All->Copythere).Add Commenton Kevin's post here: A: question about mutation data from TCGAAdd Commentbuttonmoderateback in your answer here: A: question about mutation data from TCGADelete PostSubmitbutton.Thank you!
Dear RamRS, I know I should add comment instead of simple adding my reply at the end of this thread. But there is nothing happened when I pressed the "Add Comment" button on the Kevin's post. I saw there should be a pop-down text input dialog when pressing "Add Comment" on my friend's computer. I don`t know why it does not appear on my computer!
Your browser is probably blocking javascript on the site. Users from China have faced similar problems but since you're saying your friend is able to see the Add Comment dialog, that's probably not the case. I'll move your comment myself now, but I can only move it to the top-level post, not to Kevin's answer. Please try enabling Javascript on your browser (See: How to enable javascript)