Hi,

Using [biomaRt][1] package in R, I have extracted the Transcription Start/Stop Sites of protein coding genes in human genome. So, I have a huge list of TSS. The next step is to get sequences of 1000 bp region upstream and downstream of retrieved TSS coordinates. I figured out that there isn't a function in biomaRt to download sequence upstream and downstream of the TSS.
I do appreciate if you could make a suggestion to me.


  [1]: https://www.bioconductor.org/packages/devel/bioc/html/biomaRt.html
You can use the appropiate BSGenome from Bioconductor (probably [BSgenome.Hsapiens.UCSC.hg19](http://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/) or  [BSgenome.Hsapiens.UCSC.hg38](http://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/). You should:

 1.  Transform your list of list of TSS to a GRanges object
  
 2. Get the upstrem or downstream region with [flank](https://bioconductor.org/packages/release/bioc/vignettes/GenomicRanges/inst/doc/GenomicRangesIntroduction.html)

 3. Use [getSeq](https://bioconductor.org/packages/devel/bioc/manuals/BSgenome/man/BSgenome.pdf) to retrieve the actual sequence from BSgenome


With this approach you'll only download the sequence once, when downloading the BSgenome package instead retrieveing it from the Biomart server every time you rerun the script.