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!
For DNaseI hypersensitive sites in hg19, there are tracks for various cell types on UCSC's site, with the prefix `wgEncodeAwgDnaseUw*`:

http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database

For example, for the SkMC cell line:

http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/wgEncodeAwgDnaseUwSkmcUniPk.txt.gz

The description of columns in this file is available here:

http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/wgEncodeAwgDnaseUwSkmcUniPk.sql

From this description, you could build a BED file via the following call:

```
$ wget -qO- http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/wgEncodeAwgDnaseUwSkmcUniPk.txt.gz \
    | gunzip -c - \
    | cut -f2- - \
    > wgEncodeAwgDnaseUwSkmcUniPk.bed
```

Once you have a BED file for your DNaseI dataset of interest, you can do BEDOPS set operations with this and other BED files that share the same chromosome naming scheme and genome build.