Does TCGA rna-seq data include fusion gene expression?

Question

[9521ljh]

i find some significant Chimeric(fusion gene) in DNA sequence.

And i want to compare RNA- expression level.

i read TCGA RNA-seq alignment Workflow

here: https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/

they are separating the file according to some criterion (e.g. Transcriptomic BMA, Aligned Genomic BAM, Aligned Chimeric BAM*)

However in TCGA data portal, only Gene Expression Quantification(HTseq) can be download.

Thus, i wonder, is this expression data filtering out Chimeric (fusion gene) expression ??

Answer 1

[Kevin Blighe]

The TCGA is not necessarily filtering these out... they are simply not even looking to detect these [fusion genes]. So, please feel free to re-use the TCGA data to detect fusion genes in your own study.

Kevin