Downloading a HTSeq COUNT matrix from TCGA

Question

[zamanys4]

Hi, All,

What is the best way to download gene counts (e.g. results of HTSeq, NOT normalized counts) from TCGA for a particular cancer, where all the samples are submitted by a single lab?

Answer 1

[mudasir01biotech]

First, you can select which cohort you are interested in for that please follow this link.....

https://xenabrowser.net/datapages/

or else you can use this link

https://github.com/wwysoc2/gdc-tsv-tool/blob/develop/README.md

Answer 2

[mudasir01biotech]

or this link

https://xenabrowser.net/datapages/?dataset=TCGA-SKCM%2FXena_Matrices%2FTCGA-SKCM.htseq_counts.tsv&host=https%3A%2F%2Fgdc.xenahubs.net&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443