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3.9 years ago
jmzeng1314 ▴ 130

This website is maintained by Broad Institute, the url is : http://firebrowse.org/ , and all of the TCGA data are stored in below urls :

Obevisely, you can go to these two urls directly to find what you want, but it's a little hard for the majority of us to do it. That's why they create a tool to help us to explore and download the TCGA data.

firehose_get

cd ~/biosoft
mkdir firehose && cd firehose
unzip firehose_get_latest.zip
~/biosoft/firehose/firehose_get
~/biosoft/firehose/firehose_get -tasks clinical analyses latest brca


As you can see, you should run this scripts in terminal, there are 4 parameters for firehose_get, which are :

• -tasks, to determine what kind of data to download, such as Clinical CN LowP Methylation mRNA mRNASeq miR miRSeq RPPA MAF rawMAF
• analyses or data, you have to choose one of them, to tell the tool, level 4 or level 3 data you need.
• latest or other date, you should definitely choose latest, unless you want to follow a old paper.

Examples:

1. download all of the expression data (level 3 ) for BRCA : ~/biosoft/firehose/firehose_get -tasks rna data latest brca

2. download all of the analysis results by using the rna data for BRCA: ~/biosoft/firehose/firehose_get -tasks rna analyses latest brca

Is it ver easy ?

However, to understand the data you download is not a easy thing.

Have fun with it ~~~

others

In fact, this tool is really simple, just to help you to download the data from their website, cause there are really too many data in it.

So, you can skip firehose_get, juse using wget as below :

wget -c -r -np -nH -k -L -p -A "*snp_6*hg19*" http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/BRCA/20160128/
## the same as below:
./firehose_get -tasks snp_6 stddata latest brca

tcga RNA-Seq Tutorial • 4.7k views
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tiny tip: One could use

echo 'export PATH=~/your/own/path/to/the/folder/contain/firehose_get:\$PATH' >> ~/.bashrc
source ~/.bashrc


to add firehose_get into PATH variable, then only type firehose_get is enough to execute.

NB: the PATH must end with the nearest folder name, not including firehose_get.

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Thank you for this tip.

Actually I don't like to add the software in the environment, which always mislead the newcomer to bioinformatics.

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hi,

is there a way I can get more details about the -tasks? e.g. what is available? what the abbreviation are standing for? etc..

thanks

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That info is in the original post.

-tasks, to determine what kind of data to download, such as Clinical CN LowP Methylation mRNA mRNASeq miR miRSeq RPPA MAF rawMAF

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I'm not sure if this is the full list; there is also gistic which makes me wonder whatelse is missing. Moreover, it seems that some of the keywords were depricated.