Automating Ideogram Generation For Various Organisms
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8.7 years ago

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.

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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.

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8.7 years ago

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.

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

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8.7 years ago

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

(...)

or sometimes it's called 'cytoBandIdeo'