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How to get Satellite DNA expression level from TCGA RNAseq data

Hi,

my colleague wants to determine the expression level of noncoding Satellite DNA ( ALR ) from public data sets

https://en.wikipedia.org/wiki/Satellite_DNA

But I believe the annotation of TCGA are all based on coding genes, moreover, the satellite DNA maps to many different regions of the genome. How to determine the RNA expression level?

Thanks, Ming

rna-seq
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written by Ming Tommy Tang Ming Tommy Tang

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