Question: Does TCGA rna-seq data include fusion gene expression?
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gravatar for 9521ljh
5 months ago by
9521ljh10
9521ljh10 wrote:

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 ??

ADD COMMENTlink modified 5 months ago by Kevin Blighe55k • written 5 months ago by 9521ljh10
0
gravatar for Kevin Blighe
5 months ago by
Kevin Blighe55k
Porto Alegre / London
Kevin Blighe55k wrote:

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

ADD COMMENTlink modified 5 months ago • written 5 months ago by Kevin Blighe55k
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