NGS_Where to start

Question

[fowler.trentd]

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!

Answer 1

[Devon Ryan]

1. biomart
2. Lacking other information, just do all of them.
3. Probably, but since we don't know what your actual goals are (other than doing some targeted sequencing) it's tough to say more. Since you have "ngs" in the tags, I presume you're interested in kits that will help with the targeted capture step of library preparation. I'd ask that on seqanswers rather than here.