[Genome] Ideogram mapping

[Chu, Roy]

Hi UCSC folks,

I want to map a number of features to ideograms for VERY basic
visualization purposes. Let's say, I'm interested in comparing the
locations of Alu sequences to other features. By some number of
pre-processing steps, I can determine to what loci some particular
feature I'm looking at maps to, but does the UCSC browser (or the
under-the-hood source tree) have some pre-implemented tools available
for use? My question is essentially what already-available resources
can I take advantage of to create my own ideograms?

Thanks in advance!
-Roy


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[Brooke Rhead]

Hello Roy,

The Genome Graphs tool lets you display data over an entire genome at once:
http://genome.ucsc.edu/cgi-bin/hgGenome

The user's guide to Genome Graphs is here:
http://genome.ucsc.edu/goldenPath/help/hgGenomeHelp.html

Another tool you might be interested in is the Table Browser, which you
can use to compare data from any tracks in the Genome Browser with other
tracks, or with your own data (via the use of Custom Tracks).

The Table Browser is here:
http://genome.ucsc.edu/cgi-bin/hgTables

The Custom Tracks User's Guide is here:
http://genome.ucsc.edu/goldenPath/help/customTrack.html
(Also note that in addition to creating a custom track from your own
data, you can use the Table Browser "custom track" output option to
create a custom track from the intersection of two regular Genome
Browser tracks.)

If you have further questions on any of the above tools, please feel
free to write back to the genome mail list.

--
Brooke Rhead
UCSC Genome Bioinformatics Group

Chu, Roy wrote:
> Hi UCSC folks,
>
> I want to map a number of features to ideograms for VERY basic
> visualization purposes. Let's say, I'm interested in comparing the
> locations of Alu sequences to other features. By some number of
> pre-processing steps, I can determine to what loci some particular
> feature I'm looking at maps to, but does the UCSC browser (or the
> under-the-hood source tree) have some pre-implemented tools available
> for use? My question is essentially what already-available resources
> can I take advantage of to create my own ideograms?
>
> Thanks in advance!
> -Roy
>
>
> ---------------------------------------------------------------------
>
> SECURITY/CONFIDENTIALITY WARNING:

> This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wi!

> sh to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender.
>
> ---------------------------------------------------------------------
>
>

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