I have chromosome start and end coordinates for a given chromosome. I need to translate these to locus - something like this
"11q1.4-q2.1", meaning it is on the long arm of chromosome 11, somewhere in the range from sub-band 4 of band 1, and sub-band 1 of band 2.
from wikipedia http://en.wikipedia.org/wiki/Locus_%28genetics%29
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written
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Prateek
4 answers
You can download the coordinates of the cytobands from the UCSC here.
curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/cytoBand.txt.gz" | gunzip -c
chr1 0 2300000 p36.33 gneg
chr1 2300000 5300000 p36.32 gpos25
chr1 5300000 7100000 p36.31 gneg
chr1 7100000 9200000 p36.23 gpos25
chr1 9200000 12600000 p36.22 gneg
chr1 12600000 16100000 p36.21 gpos50
chr1 16100000 20300000 p36.13 gneg
chr1 20300000 23800000 p36.12 gpos25
chr1 23800000 27800000 p36.11 gneg
chr1 27800000 30000000 p35.3 gpos25
(...)
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written
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Pierre Lindenbaum
it should be a new question, not a comment
You can use the UCSC cytoband table for this information. Just click get output and it will show you all of them and their chromosomal coordinates. Just make sure you are using the right genome builkd.
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
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written
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Leandro Lima
Heng Li wrote a generalization of such tool: https://github.com/lh3/misc/blob/master/biodb/batchUCSC.pl
You could also pipe in the region via a standard set operation with Pierre's example, e.g.:
$ curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/cytoBand.txt.gz" | gunzip -c | bedops -e 1 - <(echo -e "chr1\t10000000\t11000000")
chr1 9200000 12600000 p36.22 gneg
Obviously, if you have a bunch of regions to lookup, it is better to cache the output of curl or wget and do the set operations on that cached file. But less code is often less to go wrong and less to debug.
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written
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Alex Reynolds
I have created a website for this: https://cytob.herokuapp.com/
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written
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kindlychung •
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