Hello, I am doing a ChIP-Seq analysis and I have sorted SAM files (I used MACS). I used featureCounts and GTF file from USCS Table Browser. I have chosen "Genes and Gene Predictions" as group, "UCSC Genes" as track and "knownGene" as table. Now I have Counts matrix for my ChIP-Seq experiments and I used DESeq2. This method is used as I know from posts from Bioconductor forums.
But the problem is, my GTF file have CDS, mRNA, start and stop codons. As I know promoter regions are +1000 bp up from gene start mostly and I am not sure my GTF file have this parts or not. I also have no idea about enhancer regions.
How can I download a GTF file which also have promoter and enhancer regions. Please I am in hurry and need help.