Hello everyone !!
I'm new in the analyse of NGS data and I have ATAC-seq datas. I would like to know what is the strategies used to obtain a list with the expressed genes from the .bed files that we have after the peak calling ?
I performed peak calling with macs2 and I obtained bed files (narrowPeak) which contain the list of positions in genome where the chromatin is open. I would like to know how to obtain (from these bed files) the list of the genes which are in these regions because these should be the genes that will be expressed in my cells as the chromatin is open so we can have potentially TF binding in these regions. Then, I have to compare 2 conditions (healthy people and patient) so I have to compare 2 lists of genes that I will obtain. Is there a tool to do that ?
Thank you in advance for your help !!