Automating Ideogram Generation For Various Organisms

Question

[Alex Reynolds]

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.

[Pierre Lindenbaum]

dup of

Drawing chromosome ideogams with data

[Alex Reynolds]

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.

Answer 1

[Michael]

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.

[Alex Reynolds]

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

Answer 2

[Pierre Lindenbaum]

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 (...)