[Genome] (no subject)

[Matt Weirauch]

Hi Ray,

Try adjusting the Z score cutoff for the track on the track
description page. (You can do this by clicking on the track name.  The
field is at the top of the page.)  By default, the browser displays
TFBS with z-scores greater than or equal to 2.33 (p < 0.01).  This can
be adjusted to be as low as 1.64 (p < 0.05).  I'll bet the missing
binding sites fall somewhere in this 1.64 to 2.33 range, which is why
they are currently not being displayed in your browser.

Matt

On Mon, Mar 3, 2008 at 5:08 AM, Ray Stallings <rstallings at rcsi.ie> wrote:
> Hi,
>
>
>
>  I am having difficulty getting Genome Browser to display MYCN binding sites.
>  For example, the region chr13:90,795,999-90,802,001 contains two MYCN
>  binding sites that appear in the tables (see attached pdf). When these
>  coordinates are typed into genome browser, and the TFBS conserved box is set
>  at "full", these two MYCN sites do not appear on the browser display (see
>  attached pdf)_. This is not an isolated incident - MYCN is not appearing for
>  many regions of the genome.  Any ideas why this is so, and how I can correct
>  the problem?
>
>
>
>  Thanks
>
>
>
>  Prof. Raymond L. Stallings, PhD.
>
>  Chair of Cancer Genetics
>
>  Royal College of Surgeons in Ireland
>
>  123 St. Stephen's Green
>
>  York House
>
>  Dublin 2, Ireland
>
>  &
>
>  Programme Leader, Cancer Genetics
>
>  Children's Research Centre
>
>  Our Lady's Children's Hospital, Crumlin
>
>
>
>  PHONE: 353 1 402-8533
>
>  FAX: 353 1 402-2453
>
>
>
>
> _______________________________________________
>  Genome maillist  -  Genome at soe.ucsc.edu
>  http://www.soe.ucsc.edu/mailman/listinfo/genome
>
>