How to get karyotype information for a certain section of genome.

Question

[Chen Sun]

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.

Answer 1

[Devon Ryan]

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

[Chen Sun]

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.

[Devon Ryan]

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.

Answer 2

[Alex Reynolds]

I found Pierre's answer useful for retrieving karyotype data as a file: A: 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 -