Find mutation rates for a set of genes
1
0
Entering edit mode
4.3 years ago

Hi,

I am trying to find out how I can find the mutation frequency among various cancers for each gene in a set of around 700 genes that I'm interested in. On cBioPortal it is only possible to query 100 genes at a time and I haven't managed to download their data for my set of genes, any suggestions for how to do this?

Frida

cancer mutations cBioportal TCGA • 1.1k views
ADD COMMENT
0
Entering edit mode
4.3 years ago
poisonAlien ★ 3.1k

you would be better off with downloading MAF files for all 33 TCGA cohorts and estimate yourself.

You can use firehose to download all.

firehose_get -tasks mutsig analyses latest

This would download all MutSig results including stable maf file that broad uses for their downstream analyses.

ADD COMMENT
0
Entering edit mode

Thanks! I will look into that.

ADD REPLY

Login before adding your answer.

Traffic: 2450 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6