Appendix: Obtaining a BED of Telomere sequences

Rationale

The Rhee and Pugh, 2011 paper used genomic features to filter out results from peak-calling. We want to do this as well.

A good approach seems:

  • get list or lists as Bed file fom YeastMine
  • Uses Bedtools with intersectBed -v to filter out those summits that are in telomeres.

Obtain Telomeric sequences as a BED file from YeastMine

Go to YeastMine

Scroll down to where you see Lists.

YeastMine Lists

Among the Lists listed there should be Telomeres. If not, click on More lists and examine the list of lists.

Click on the Telomeres list link.

Click on the Download button.

Download list button

Choose UCSC-BED (Browser Extensible Display Format) from the choices.

Choose BED format

Now either click green Download File button at the bottom to download to your local computer. You could then use scp to upload as illustrated here it to an Amazon EC2 instance, for working on the worksop analysis example.

Alternatively, click on the Destination File tab in the toolbar on the left side of the Download Results window.

get URL to download

Note that there is a URL that makes uploading to an EC2 instance on Amazon Web Services even easier. In fact you can click copy to clipboard and then paste after the following text once you ssh into your working directory on your instance. For example,

wget http://yeastmine.yeastgenome.org/yeastmine/service/query/results?format=tab&start=0&token=i1r4ud70h133R7ned6x2&columnheaders=1&query=%3Cquery+model%3D%22genomic%22+view%3D%22Telomere.primaryIdentifier+Telomere.secondaryIdentifier+Telomere.symbol+Telomere.name%22+%3E%3Cconstraint+path%3D%22Telomere%22+op%3D%22IN%22+value%3D%22Telomeres%22+code%3D%22A%22+%2F%3E%3C%2Fquery%3E

Note that the above command is just an example for constructing your command. The API token in the URL is temporary and expired long ago.