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
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 ??