Dear Organizers
In the summary of DNase processing you wrote:
"Duplicate reads were then marked with Picard MarkDuplicates and removed."
Many researchers think that by removing the duplicates we are loosing the information about real peak intensity.
In my lab the consensus is not to remove duplicates.
Is it possible to provide a FASTQ files that we can process with our own pipelines or your protocol is mandatory?
Created by Ramil Nurtdinov n.ramil Sorry. You will need to use what we've provided.
Thanks
Anshul