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 ??
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written
by
9521ljh •
1 answer
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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