[Genome] [UCSC genome browser] Question on Yeast annotation

[Joo Sang Lee]

Hello, all.

I am analyzing yeast genome using UCSC genome browser. I want to remove
coding regions from yeast genome based on annotation file. In UCSC genome
browser, they provide annotation file called sgdGene.txt. It has indexes of
coding and exon regions in each chromosome. But the problem is some of the
indexs are larger than the number of nucleotides in the chromosomes. So, I
cannot locate the coding and exon region. Here is the link to UCSC genome
browser.
http://hgdownload.cse.ucsc.edu/goldenPath/sacCer1/database/

They may provide better annotation file, but I am not sure which to use.
Please give me some advice. I look forward to any comment or information.
Thank you much.

Sincerely,

Joo Sang Lee
Department of Physics
Northwestern University