Question: How to get karyotype information for a certain section of genome.
0
gravatar for Chen
3.5 years ago by
Chen590
Chen590 wrote:

Hi all!

I have some sections of genome location such as chr16:100-300, chr17: 1000-2000. I want to know how can I get the corresponding karyotype information. As I have large amount of genome location sections, I want to whole file of genome location to corresponding karyotype. 

For instance, chr16:100-300 may corresponding to 16q1, which chr17: 1000-2000 may corresponding to 17q2 etc.

The location information is from hg19.

 

 

karyotype • 796 views
ADD COMMENTlink modified 3.5 years ago by Alex Reynolds21k • written 3.5 years ago by Chen590
0
gravatar for Devon Ryan
3.5 years ago by
Devon Ryan73k
Freiburg, Germany
Devon Ryan73k wrote:

That information is available in the cytoBandIdeo table from the UCSC table browser (group: "Mapping and Sequencing", track: "Chromosome Band (Ideogram)").

ADD COMMENTlink written 3.5 years ago by Devon Ryan73k

Thank you, how can I get the whole file of genome location to karyotype? as I have many sections, it will not be realistic to query them one by one in UCSC browser. 

ADD REPLYlink written 3.5 years ago by Chen590

You can just download the whole file (note the "Get Output" button) from the table browser or just get it via FTP. There are a variety of way to match a given region to that file, then. If you're in R already, you can findOverlaps(), or you could use bedtools or bedops (to give just two examples) from the command line.

ADD REPLYlink written 3.5 years ago by Devon Ryan73k
0
gravatar for Alex Reynolds
3.5 years ago by
Alex Reynolds21k
Seattle, WA USA
Alex Reynolds21k wrote:

I found Pierre's answer useful for retrieving karyotype data as a file:  Automating Ideogram Generation For Various Organisms

After that, I would convert to BED and use bedops to do a set operation on regions-of-interest:

$ echo -e "chrN\tA\tB" | bedops --element-of -1 someKaryotype.bed - 
ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by Alex Reynolds21k
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