Question

Giemsa stain annotation/nomenclature for UCSC cytoband tracks

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metamaden ▴ 10

@madensean-8348

Last seen 12 months ago

United States

Hi,

Background: This is a general question regarding UCSC's provided cytoband info, specifically whole-genome Giemsa Stain track information, as provided here:

https://genome.ucsc.edu/cgi-bin/hgTables (assembly = hg19; group = Mapping and Sequencing; track = Chromosome Band (ideogram); type = cytoBandIdeo).

My question: Where can I find annotations/nomenclature for the gieStain results in the table schema? ie. how was the values histogram calculated and what does it mean for DNA sequence/density.

Tags: I've tagged modules that cite UCSC's hg19 cytoband track, in case their users/devs happen to know the answer.

Thanks!

Sean

UPDATE: Slightly more info is available here: http://genome.ucsc.edu/goldenPath/help/trackDescriptions.html

ucsc ucsctrack ggbio Gviz hg19 • 3.0k views

ADD COMMENT • link updated 7.8 years ago by maximilianh ▴ 10 • written 7.8 years ago by metamaden ▴ 10

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I'm not sure this is a Bioconductor question, is it? If you just want to know things about UCSC tables, you should ask the UCSC people, because it's their website.

ADD REPLY • link 7.8 years ago James W. MacDonald 67k

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That's a fair point. My question comes up because I've noticed the cytobands being used in documentation for several Bioconductor packages, and I'm interested in the Giemsa Stain cytobands specifically, not UCSC tables in general. I will direct my question to UCSC as well.

Sean

ADD REPLY • link 7.8 years ago metamaden ▴ 10

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UCSC is here!

ADD REPLY • link 7.8 years ago maximilianh ▴ 10

score 1 · Answer 1 · 2017-02-21

You have found an outdated page with descriptions and we will remove this old page.

The real track descriptions can be found if you click on a track from within the browser.

The "chromosome bands" page is this one:

http://genome.ucsc.edu/cgi-bin/hgTrackUi?c=chr21&g=cytoBand

It says that the methods for this track are in Furey and Haussler 2003.

Does this resolve the question?