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2 hours ago by

Hi,

I want to quantify the leads in my defined region.

This is not a gene, but an enhancer region. (from ENCODE)

The data is a bam file that maps total RNA-seq using tophat.

I want to measure the expression of a region that is thought to be an enhancer RNA that is not defined in human gtf.

So I wondered if I could use the gffs for the regions I want to use for quantification.

But, I am not sure which tool to use and how.

Thanks you.



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