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How to get each exon counts from TCGA

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

rna-seq tcga alignment gene
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updated by EagleEye EagleEye • written by siyangming • siyangming

2 answers

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.

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written by Martombo Martombo

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

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written by EagleEye EagleEye

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

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written by Martombo Martombo

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