Hello, Satish,
We do not have a gene density table in our database, but if you have
some command-line access and do not mind writing a little script, you
could use the knownCanonical table on our public mysql server to
generate it. knownCanonical maps only one gene per locus in the genome,
ignoring isoforms that would confuse a gene count analysis. Here is a
piece of pseudocode to get you started:
foreach chrom (iterate through all chroms)
foreach interval (10 Mb interval on chrom)
mysql -h genome-mysql -u genome -N -e "SELECT COUNT(*) FROM
knownCanonical WHERE chromStart > intervalStart AND chromStart <
intervalStart + 10000000" hg19 >> file
end
end
You would actually need to capture the result in each loop in a variable
and send the chrom, chromStart and chromEnd to the file along with the
value.
You could then build a custom track from the results, if you chose.
see:
http://genome.ucsc.edu/goldenPath/help/bedgraph.html
For your second question, you will want to use the Conservation track
on the rat rn4 browser to see a plot of conservation. The Most
Conserved track shows the regions above a threshhold level, but does
not display a graphic that you would call a plot.
Thanks for being a user of the Genome Browser. If this reply does not
fully answer your question, please do contact us again via the mailing
list.
Best wishes,
--b0b kuhn
ucsc genome bioinformatics group
On 1/17/2011 10:36 PM, satish sati wrote:
> To UCSC
>
> We are a research group at Institute of Genomics and Integrative Biology,
> Delhi, India. We need to map gene density (not ref seq genes), with our
> data. Could you please suggest us from where we can download or access the
> track for gene density. Also we are interested in plotting conservation
> track among rat and other mammals in a single track. For this purpose what
> track we should use (most conserved or conservation)
>
> Waiting for your reply
> Thank You
> Satish Sati
> Senior Research Fellow
> Institute of Genomics and Integrative Biology,
> Delhi, INDIA
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