Question: Giemsa stain annotation/nomenclature for UCSC cytoband tracks
0
gravatar for maden.sean
2.5 years ago by
maden.sean10
United States
maden.sean10 wrote:

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

ggbio gviz ucsc hg19 ucsctrack • 841 views
ADD COMMENTlink modified 2.5 years ago by maximilianh10 • written 2.5 years ago by maden.sean10

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 REPLYlink written 2.5 years ago by James W. MacDonald50k

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 REPLYlink written 2.5 years ago by maden.sean10

UCSC is here!     

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by maximilianh10
Answer: Giemsa stain annotation/nomenclature for UCSC cytoband tracks
1
gravatar for maximilianh
2.5 years ago by
maximilianh10
UCSC
maximilianh10 wrote:

You have found an outdated page with descriptions and we will remove this old page.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

ADD COMMENTlink written 2.5 years ago by maximilianh10
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