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.
|Exons plus||bases at each end|
|Introns plus||bases at each end|
|5' UTR Exons|
|3' UTR Exons|
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!