[Genome] Phastcons scores for introns from Table Browser

[Ann Zweig]

Hello Lax,

	Yes, you can do this in two steps using the Table Browser.  First, you will 
create a Custom Track made of the introns of the genes you are interested in. 
Then you will intersect the phastCons track with your Custom Track to get the 
scores for each base in your Custom Track.

Step One.  Create a Custom Track of the introns of the genes you are interested in:
- From the Table Browser, choose UCSC Genes and paste your list of IDs into the 
"identifiers (names/accessions)" location.
- Choose Custom Track as the output type, then choose to create one BED record 
per "Intron".
- Press 'get custom track in table browser' button.

Step Two.  Intersect the phastCons track with your Custom Track:
- From the Table Browser, choose the phastCons track for your assembly (e.g. for 
hg18 it is called phastCons28way).
- Create an Intersection with your Custom Track.
- Choose "data points" as the output format.
- Press 'get output' button.

	This will give you a base-by-base phastCons score for every intron position in 
your list of genes.

	I hope this information is helpful to you.  Please don't hesitate to contact 
the mail list again if you require further assistance.

Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu

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Lakshmanan Iyer wrote:
> Hi
> Is there way to get the phastcons scores for the introns of a list of UCSC
> transcript ids via the Table browser?  If not could you please suggest an
> alternative?
> -Best
> -Lax
> 
>  Lakshmanan (Lax) Iyer, Ph.D.
>  Research Assistant Professor
>  Department of Neuroscience
>  Senior Manager, Computational Genomics Core
>  136 Harrison Ave
>  Boston, MA 02111
>  Phone: (617) 636-0329
>  Fax: (617) 636-2413
>  Lax.Iyer at tufts.edu
>  http://www.neurosci.tufts.edu/research_asst_profs/iyer/iyer.html
> 
>  Assistant Professor
>  Molecular Cardiology Research Center
>  Tufts Medical Center
>  800 Washington Street, Box 080 Boston,
>  Boston, MA 02111 
>  liyer at tuftsmedicalcenter.org
>  Phone: 617-636-1441
>  http://160.109.101.132/mcri/StaffDirectory/PrincipalInvestigators/Lakshmana
> n.Iyer
> 
> 
> 
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