Greetings - Help Please! Paul Freiman

[Paul Freiman]

Greetings,
I am a beginner at this and am working on a school project!
I have been scouring the web for answers but have been totally stumped!
I am trying to understand how the coordinate system for the human reference genome 18 works?
Mainly:
1) How do I figure out the first position?
2) How do N's affect the positioning?
3) how do masked nucleotides affect the positioning? (repeat masker)
Any help would be throughly appreciated!
Thanks,
Paul Freiman
NYU

[Pauline Fujita]

Hello Paul,

You might find this tutorial on the Genome Browser to be a useful
starting point:

http://www.openhelix.com/cgi/tutorialInfo.cgi?id=27

In response to your specific questions:

1) The first position of a chromosome in the Genome Browser is 1. To
see it, navigate to the beginning of a chromsome (chr1:1-20, for
instance) and look at how the bases are numbered. Note that in our
tables, though, the first base is numbered 0. See this page to read
about why: http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms.

2) Ns take up space, just as A, C, G, and T do.

3) Masking does not affect positioning.

Hopefully this is enough to get you started. If you have further
questions please feel free to contact the mailing list again at
gen...@soe.ucsc.edu.

Best regards,

Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu

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