the1000genomesbrowsertutorial.docVIP

The 1000 Genomes Browser Tutorial http://1000/ Updated on 05/05/2011 To facilitate immediate analysis of the 1000 Genomes data by the whole scientific community, the Ensembl genome browser was adopted to display SNP calls made by the project, even before they are integrated into dbSNP. The look and feel of the 1000 Genome Browser are very similar to the Ensembl browser. We will cover some basic browsing tips in this tutorial. Please refer to Ensembl tutorials for greater details (/info/website/tutorials/index.html). Please note that the 1000 Genomes SNPs have been submitted to dbSNP and will each be allocated a dbSNP rsID. Until that point any SNP IDs on the 1000 Genomes Browser are temporary and will not be maintained. Getting Started with the 1000 Genomes Browser ? Go to . ? click on the “Browser” tab you will get to the Browser home page: ? click on the browser link / you will see the following search box: ? Enter a gene name/symbol/identifier in the text box. Gene PTPN22 is used as an example in this tutorial. ? Click [Go]. When you search for a chromosome region, the browser will jump to a chromosomal location page centers around the region you specified. When you search for a gene or gene product, the search results can be in one or all of the following categories: Gene Transcript Peptide ? Click on a gene in the search result page takes you to a gene page ? Click on a transcript in the search result page takes you to a transcript page ? Click on a peptide in the search result page takes you to a peptide page We will go through gene page, transcript page and chromosomal location page in the following sections. Peptide page is very similar to transcript page in terms of variation display so we will not discuss it separately. At the end, we will describe briefly how to export data to your local machine and how to add your own tracks of data; we will also introduce two useful tools – Variation Effect Predictor and Data Slicer.