Hi community,
My colleague recently tries to compare enhancer activity of control and knockdown cell line using total RNA-Seq. Total RNA-Seq data was used to see the abundance of transcripts as controlled by the enhancer (estimated using https://www.weizmann.ac.il/Biological_Regulation/IgorUlitsky/EPC), in turn estimating the activity of the enhancer. The output data show the + strand and - strand read counts for each enhancer-controlled region (or CPM).
Is it valid if I use DESeq2 or other RNA-Seq analysis tools, treat each enhancer as a gene, and compare the counts in control and the knockdown to see if there is any change in + strand, - strand and in combination? I would be performing 3 separate analyses for each strand (and combined). It is just for getting a quick look at what targets we can get.
Thanks for your help in advance.
Edit1: found some publications using DESeq2 for differential eRNA expression analysis. But again, is it valid? (Paper found here) Edit2: Due to the nature of eRNA there could be a lot of low count regions. Is there an appropriate threshold for filtering enhancer with low eRNA counts? Or is it arbitrary?
