Hi Dafil,
Using the Table Browser, you can obtain the upstream and downstream
regions around the centromeres and telomeres in two separate queries
(one for upstream and one for downstream). Click on "Tables" on the blue
bar on the top of the main page, select the hg18 human assembly, and
then make the following selections:
group: mapping and sequencing tracks
track: gap
table: gap
region: genome
filter: click "create"; enter "centromere telomere" (no quotes) in
the "type does match" box; click submit.
output format: custom track
output file: enter the name you want the data to have (e.g.
upstreamRegions)
Click "get output." Enter a name and description for your custom track
(such as " name=upstreamRegions" and "description=upstream from
Telomeres and Centromeres"), select "Upstream by," and enter the number
of upstream bases you want in the adjacent field. Click "get custom
track in file" for a the list of positions upstream of centromeres and
telomeres. Save the file. Repeat the same process for the downstream
regions except name appropriately and select "Downstream by" and enter
the number of downstream bases in the adjacent field.
Now you should have two files, one with regions upstream of the
centromeres and telomeres and one with regions downstream of the
centromeres and telomeres.
I hope this information is helpful.
Katrina Learned
UCSC Genome Bioinformatics Group
[email protected] wrote, On 11/26/10 05:45:
> Hi,
> I am just wondering if anyone can help with a query,
>
> what are the coordinates for:
> 1. pericentromeric region
> 2. and subtelomeric region for the entire genome (hg18 coordinates)?
>
> that would be a great help.
>
> regards,
> -dafil
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
>
_______________________________________________
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