Question: Automating Ideogram Generation For Various Organisms
0
gravatar for Alex Reynolds
6.4 years ago by
Alex Reynolds29k
Seattle, WA USA
Alex Reynolds29k wrote:

I would like to automate the process of making an SVG representation of an individual ideogram, in the linear form seen (for example) at the top of a UCSC Genome Browser session. What data sources should I use to get the banding data?

I'd also be interested in any information about the format the data are presented in, so that I can translate it into a figure that includes band start/stop, centromere position, p/q arms, coordinate system data, etc.

• 2.7k views
ADD COMMENTlink modified 6.4 years ago by Pierre Lindenbaum123k • written 6.4 years ago by Alex Reynolds29k

dup of

Drawing chromosome ideogams with data

ADD REPLYlink written 6.4 years ago by Pierre Lindenbaum123k

Sorry, to be clearer: I'm not looking for third-party packages to draw them, but the actual sources of data that go into them, so that I can render a figure with my own code.

ADD REPLYlink written 6.4 years ago by Alex Reynolds29k
3
gravatar for Michael Dondrup
6.4 years ago by
Bergen, Norway
Michael Dondrup46k wrote:

The ideogram is drawn from information stored in a "karyotype" track. ggbio can fetch this track automatically from UCSC, if it exists, and draw the ideogram. plotIdeogram is the function to look at.

ADD COMMENTlink modified 6.4 years ago • written 6.4 years ago by Michael Dondrup46k

It looks like some source code might be here: http://bioconductor.org/packages/devel/bioc/html/ggbio.html

ADD REPLYlink written 6.4 years ago by Alex Reynolds29k
0
gravatar for Pierre Lindenbaum
6.4 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum123k wrote:

In the UCSC browser, the cytoBand are located in the cytoBand database:

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/cytoBand.sql

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/cytoBand.txt.gz

(...)

http://hgdownload.cse.ucsc.edu/goldenPath/mm10/database/cytoBand.sql (...)

or sometimes it's called 'cytoBandIdeo'

http://hgdownload.cse.ucsc.edu/goldenPath/canFam3/database/cytoBandIdeo.sql (...)

ADD COMMENTlink written 6.4 years ago by Pierre Lindenbaum123k
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