Hey,
I often see cytogenic coordinates written as e.g.
3q26
If I put this into the UCSC genome browser I see this region corresponds to:
chr3:160,700,001-182,700,000
My question: Is there an easy was to jump between the two using R? Or a simple way to calculate one from the other I could implement?
Thanks!
•
written
by
Jimineep •
You can use your favorite mysql wrapper in R.
From location to cytoband using the commandline:
mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19 -e
"select name from cytoBand where chrom = 'chr3' AND chromStart <= 182700000
and chromEnd >= 160700001"
from cytoband to location:
mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19 -e
"select chrom, min(chromStart), max(chromEnd) from cytoBand where
name like 'q36%' group by chrom;"
Thanks! Although this can't be an uncommon task, if I can get it to work I might stick something on R-forge/CRAN
A note about the 'location to cytoband using the commandline' section. If you don't have a point, but an interval, you'll need to check for overlap.
In this case, check http://stackoverflow.com/questions/325933/determine-whether-two-date-ranges-overlap for the most efficient way to do this.
So, something like this (for finding gene names)
SELECT name2 FROM refGene WHERE chrom=$chr AND ( txStart<=$end AND txEND>=$start)";
or this (for finding cytoBands)
SELECT name FROM cytoBand WHERE chrom=$chr AND (chromStart <= $end and chromEnd >= $start)";
•
written
by
Dan (findingdan) •
You could also directly download the coordinates of the cytoBands:
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/cytoBand.txt.gz
Hi all.
Based on the hints given here, I created a script to do that.
https://github.com/lelimat/bioinfo/blob/master/region_to_cytoband.sh
The usage is
bash region_to_cytoband.sh chrom:start-end
or
bash region_to_cytoband.sh chrom start end
Please feel free to improve.
Regards,
Leandro
•
written
by
Leandro Lima
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I should add that I have seen this, I wanted to ask if there was an easy way to do it in R without downloading files
http://biostar.stackexchange.com/questions/4363/how-to-obtain-chromosome-locus-from-coordinates