Hi, I am studing eRNA using RNASeq data and I would like to know how define the eRNA track. Is it sufficient to consider just enhancer regions or it is better consider ehnacer regions plus 2-3kb upstream-downstream of them? At moment I am considering the track downloaded from Enhancer Atlas.
I am not sure what do you mean by eRNA track , but to define eRNAs from RNA-Seq, you can get some inspiration from A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples
Enhancers are usually 500 to 1000bp. Considering +/- 2 or 3kb is a bit too much.
Just check this pipeline for enhancer RNA quantification from RNA-seq,
http://fun-science.club/PET/
You can also check the paper: Wu, Y, Yang, Y, Gu, H, et al. Multi‐omics analysis reveals the functional transcription and potential translation of enhancers. Int. J. Cancer. 2020; 1– 15. https://doi.org/10.1002/ijc.33132
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
version 2.3.6
For "eRNA track" I mean the track against to count RNA-Seq reads. Is it sufficient consider the enahcer coordinates or is it necessary to enlarge each region?
You can just consider enhancer region. But, its not as simple as counting the RNA reads mapped on to "enhancer" definition. You should be careful in defining eRNAs, and I would suggest to read the paper below to get an idea about defining eRNAs from RNA-Seq data.
Ok. Thank you very much for your suggestion.
If it solved your question, accept the answer so that the post will be "closed"