I am interested in sequencing the promoter regions, the exons and the splice junctions of three genes. What is the best way to find the locations of all the exons and generate a bed file using hg19 as the reference? Also, I understand that each gene may generate multiple transcripts, is it best to use the sequence that produces the longest transcript or the RefSeq gene? Finally, what questions should I be asking that I am not?
Thank you all!!