Does TCGA rna-seq data include fusion gene expression?
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2.9 years ago
9521ljh ▴ 50

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 ??

sequencing RNA-Seq sequence next-gen • 710 views
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2.9 years ago

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

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