I've noticed that the script getEGC.pl calls a file called "./AllgenesenhspairsScore.bed". However, this file is not available in the repository nor is it created in earlier scripts and we do not provide this as input when we call EAGLE.pl. My understanding is that, without this we cannot get enhancer-gene correlation scores for out input enhancers. Do you have an example of how you would make this file or what it would look like?
Hello,
I've noticed that the script getEGC.pl calls a file called "./AllgenesenhspairsScore.bed". However, this file is not available in the repository nor is it created in earlier scripts and we do not provide this as input when we call EAGLE.pl. My understanding is that, without this we cannot get enhancer-gene correlation scores for out input enhancers. Do you have an example of how you would make this file or what it would look like?
Thank you, Allison