How to get each exon counts from TCGA

Question

[siyangming]

I only get each gene counts from the TCGA website，how can I get the each exon counts of each genes？

Answer 1

[Martombo]

For those passing by this question: at the time of speaking (end of 2017) TCGA exon counts data are not present on the harmonized data portal, so if you want to get these data you'll have to scavenge through the legacy portal, where different genome versions and annotations are used. You can filter for "exon quantification" in Files - Data Type.

Answer 2

[EagleEye]

Hi, Try Synapse project, https://www.synapse.org/#!Synapse:syn300013/files/

[Martombo]

thanks, that looks like a neat repository. I can't find exon counts however, while they have isoform and gene data.