[Genome] regions annotations

[Brooke Rhead]

Hello Vesko,

There is not a quick way to get the information you need, but you should 
be able to get something close by making a series of custom tracks and 
intersecting them in the Table Browser.

You can upload your regions of coordinates in a BED file into the Genome 
Browser by making a custom track:
http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks

Then you can use the Table Browser to make custom tracks of each type of 
region you are interested in.  The introns and exons should be 
straightforward: when you have selected a gene track from the "Genes and 
Gene Prediction Tracks" group and selected "output format: custom 
track", you are given the option to select particular regions.  Make one 
custom track where you "create one BED record per Exon" and make another 
where you "create one BED record per Intron".

(If you want, you can collapse overlapping regions by intersecting each 
custom track with itself and choosing the option for base-pair-wise 
union.  For instance:
  * Base-pair-wise union (OR) of INTRONS and INTRONS
Note that doing this will cause the gene name information associated 
with the items in the track to be lost.)

To get a custom track of the intergenic regions, first combine the 
introns and exons custom tracks using the "Base-pair wise union (OR)" 
intersection option.  Now intersect the new custom track (of both 
introns and exons) with itself, but choose to "complement (the new 
track) before base-pair-wise intersection/union".  This is described in 
more detail in this previously-answered mailing list question:
http://www.soe.ucsc.edu/pipermail/genome/2007-October/014783.html

You can make custom tracks of gene flanking regions by choosing a gene 
track in the Table Browser, and then choosing to "Create one BED record 
per: upstream by (some number) bases", and then " Create one BED record 
per: Downstream by (some number) bases".  The number of bases is up to you.

Once you have generated custom tracks for each type of region (introns, 
exons, intergenic regions, flanking regions), you can interesect your 
initial custom track of regions one at a time with the custom track of 
each type of region.

There may be a better way to do all of this using Galaxy.  You will need 
to write to their helpdesk for help using the Galaxy tools.

--
Brooke Rhead
UCSC Genome Bioinformatics Group


Vesselin Baev wrote:
> Dear all,
> is there a way (in UCSC TABLES, or Galaxy) to upload a regions with
> coordinates (in a BED file) and get  the annotation (if there is) what this
> redion is part of - intron, exon, intergenic, flanking gene names .....
> 
> 
> Vesko
>