Hi!
I need to plot some genomic locations in context of their distances from transcription start site, CpG islands and Dnase hypersensitive sites.
Question1) Can anyone please tell me how I can get ucsc/refseq transcription start site with 1kb up- and downstream flank from ucsc table browser? In the output, i see the following options, I am not clear which options to choose to get what I want. If I just retrieve base pairs upstream to genes, I will miss the alternate TSS.
"
Whole Gene | |
Upstream by | bases |
Exons plus | bases at each end |
Introns plus | bases at each end |
5' UTR Exons | |
Coding Exons | |
3' UTR Exons | |
Downstream by | bases |
"
Question 2) How can I get lists of CpG islands and DNase hypersensitive sites of human genome?
Thanks a lot for your time and help!