Question: A question about the coordinate system in the yeast database
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gravatar for Xuekui Zhang
8.1 years ago by
Xuekui Zhang20
Xuekui Zhang20 wrote:
Dear list, I am working with yeast genome "Saccharomyces cerevisiae". My sequences are aligned to reference genome of version "sacCer2". I found the ensembl annotation of genes has 3 versions, including SGD1.01, EF2, and EF3. I would like to use same coordinate system for aligned reads and annotated genes. Could anyone explain how to match the two different systems (i.e. sacCer1/sacCer2 vs SGD1/SGD2/EF3)? Thanks! Xuekui -- Xuekui Zhang, PhD Candidate Department of Statistics 333-6356 Agricultural Road University of British Columbia Vancouver, BC, V6T 1Z2 Phone: 604-822-2924 Fax: 604-822-6960 https://www.stat.ubc.ca/People/Home/index.php?person=xzhang [[alternative HTML version deleted]]
annotation yeast • 539 views
ADD COMMENTlink modified 8.1 years ago by Hervé Pagès ♦♦ 14k • written 8.1 years ago by Xuekui Zhang20
Answer: A question about the coordinate system in the yeast database
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gravatar for Hervé Pagès
8.1 years ago by
Hervé Pagès ♦♦ 14k
United States
Hervé Pagès ♦♦ 14k wrote:
Hi Xuekui, On 11-08-08 04:04 PM, Xuekui Zhang wrote: > Dear list, > > I am working with yeast genome "Saccharomyces cerevisiae". > > My sequences are aligned to reference genome of version "sacCer2". > I found the ensembl annotation of genes has 3 versions, including SGD1.01, EF2, and EF3. > > I would like to use same coordinate system for aligned reads and annotated genes. > > Could anyone explain how to match the two different systems (i.e. sacCer1/sacCer2 vs SGD1/SGD2/EF3)? Right. Ensembl is currently using the EF3 assembly from February 2011, which is more recent than sacCer2. Working with two different coord systems sounds tricky and you'll probably make your life much easier by using the same coord sys for alignment and annotations. So why not align your sequences to EF3? Or use annotations from the "Ensembl Genes" track provided by the UCSC genome browser (for sacCer2) if realigning your sequences is not an option for you? Cheers, H. > > Thanks! > Xuekui > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319
ADD COMMENTlink written 8.1 years ago by Hervé Pagès ♦♦ 14k
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