[Genome] How to figure out chromosome lengths

[Kayla Smith]

Carl,

The chromInfo table for the hg18 assembly will give you the information 
you are looking for.

Click on "Downloads" on the navigation bar on the left hand side of the 
main page, then click on "Human", and on "Annotation Database".  Scroll 
down until you find chromInfo.txt.gz.

Or use this link: 
http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/chromInfo.txt.gz

Another place to easily access chromosome length is on the gateway page 
for each assembly.  There is a "sequences" link that will show you the 
length of each chromosome.

Here is the link for the gateway page:
http://genome.ucsc.edu/cgi-bin/hgGateway

Please don't hesitate to contact us again if you require further 
assistance.

Kayla Smith
UCSC Genome Bioinformatics Group


Ton, Carl C wrote:
> Hi
> 
> I've been folowing this thread, and found the discussion very helpful. However, I'm interested getting a table of the lengths of chromosomes using the human genome Build36.1. How would I go about doing that?
> 
> Thanks,
> 
> Carl
> ---------------------------------------------
> Hello Shan-
> 
> 	You can locate the centromeres via the "gap" table in the Table
> Browser.  To go to the Table Browser, click the "Tables" link from the 
> navigation bar.  Set up the selections to include galGal2 (Feb. 2004), then 
> select the gap table, then click the 'filter Create' button.  Set the "type" 
> field to "centromere".
> 
> #chrom	chromStart	chromEnd
> chr1	69458565	70958565
> chr2	51099589	52599589
> chr3	11514083	13014083
> chr4	18442166	19942166
> chr5	3100873	4600873
> chr7	7193916	8693916
> chr8	9913109	11413109
> chrW	195830	695830
> chrZ	19878666	21378666
> chr10	2006967	3506967
> chr11	2591139	3091139
> chr12	2826948	3326948
> chr17	4298663	4798663
> chr23	5166127	5666127
> chr26	3743731	4243731
> chr28	4231479	4731479
> 
> 
> 	You can follow a similar procedure to identify the telomeric
> locations as well (just substitute the word "telomere" for
> "centromere").
> 
> 	Hope this answers your question.  Please feel free to write back to the list if 
> you need more help.
> 
> 
> Regards,
> 
> ----------
> Ann Zweig
> UCSC Genome Bioinformatics Group
> http://genome.ucsc.edu
> 
> 
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