some question about the paper
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Sorry to bother!
I 'd appreciate a lot if you can reply !!
I have read your paper , which is an excellent work. However, I might not comprehend the paper very well, and do have some question in the CAGE Tag Analysis part.
My question is that the paper has showed that the inactive promoters showed low percentage of CAGE tag support. And CAGE-seq data is thought as the golden standard of the transcriptom start sites, hence whether inactive promoters' start site called by proActiv was less possible to be real transcriptom start site?
And I tried to apply the proActiv to other species, the result showed low percentage of overlapping with CAGE-seq data.
If it is available, please reply. Your reply will do me a lot favor, appreciate again!
Best wishes!!!
Hi @ninjaxfy all promoters used by proActiv are annotated, whether they are active or not does not mean they are real or not (they could for example be active in a different tissue). Inactive promoters show low levels of transcription, similar to start sites with low CAGE tag support. I hope that helps!