Problem on getting rat(rn6) centromere coordinates

[胡洸瑜]

Dear UCSC crew:

     I'm writing this letter to ask a problem when I use the table browser to get coordinates of rat(rn6) centromere. The ".bed" file which I downloaded says "# No results returned from query". Besides, I tried human hg38, and got the same answer. However, when I used hg19, I can get correct bed file which contains "chromosome, start, end". I didn't change any other settings besides "assembly(hg19）". Considering this, I wonder if there's any bug on the query of getting coordinates of different version of genome(e.g. rn6, hg38).   
     I'm looking forward to your gentle help. 
     Best Regards,

     Dr. Joshua Hu
     Air Force Medical University
     Xi'an, China
     

 

[Brian Lee]

Dear Joshua,

Depending on the approach you are taking you should see this information for hg19 and hg38. One approach in the Table Browser is to use the cytoBand and cytoBandIdeo tables which provide information to draw the graphic above the main Browser display to indicate the centromere and Giemsa staining where "acen" is used to denote centromeric.

By selecting the Mapping group in the Table Browser and the Chromosome Band (Ideogram) track and cytoBandIdeo or the cytoBand table you can export results and look for the acen regions (two regions displaying like a triangle toward the middle).

Another option is to directly access the files with the command-line and select those regions, below are commands that pull the acen regions for chr1 for hg19 and hg38, but these same selections can be done with the Table Browser:

curl -s "http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/cytoBand.txt.gz" | gunzip -c | grep acen | grep -w chr1
chr1    121500000    125000000    p11.1    acen
chr1    125000000    128900000    q11    acen

curl -s "http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/cytoBand.txt.gz" | gunzip -c | grep acen | grep -w chr1
chr1    121700000    123400000    p11.1    acen
chr1    123400000    125100000    q11    acen

If you do the Table Browser selections for rn6 for rat you will note there are no acen regions denoted. Or if you do the command-line approach you will see no annotations returned:

curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/rn6/database/cytoBand.txt.gz" | gunzip -c | grep acen 
(no hits)

A member on our team notes that many of the mouse and rat chromosomes are acrocentric, that is they are at the ends of the chromosomes, not the middle like humans, explaining the lack fo the acen annotations.

If you use the cytoBandIdeo approach you may be interested in looking at this previous mailing list question that explains the acen, stalk, and gvar entries that help control the shading in the graphical display: https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/Lymdl_dJvYQ/oSNOTHWVr98J.

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further public questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

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Brian Lee

UCSC Genome Browser  

UC Santa Cruz Genomics Institute |  Revealing life’s code.

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[Brian Lee]

Dear Joshua,

You might be using the gap track to obtain the centromere information for hg19, in which case for hg38 you will notice it is missing. You might be interested in this previous MLQ where we discuss a new centromere track for hg38: https://groups.google.com/a/soe.ucsc.edu/g/genome/c/c9eZ_fywMbo/m/jBTfdXOyAgAJ

All the best,