|SNPscan||Click the following link to view (or save to your hard drive) a text file with Affymetrix 50K SNP data from three individuals. Once this text file has been saved to your hard drive, go to the SNPscan page, and (in Step 1) browse to choose this text file to upload. In step 2, enter "samples_50K.txt" (without the quotation marks). Your output will look like this (click to enlarge): You can see that the bottom track is from a male (with a lower copy number on the X chromosome) with uniparental isodisomy on the long arm of chromosome 1 (note the blue region showing homozygosity, without any change in chromosome copy number).|
|KKI SNP analysis tools|
Click here for a file with 100K data (10 MB, consisting of both 50K Hind and 50K Xba data from two normal individuals). Here is a 100K cancer data set (17 MB in size), consisting of 3 breast cancer cell lines and a normal reference set, originally posted by Affymetrix on its website. You can find various chromsomal abnomalities in these three cancer cell lines.
Click here for a 10K sample file of one individual; this file can be processed relatively quickly by SNPscan. [You can use this 10K (single individual) file for the SNPscan tool, or, delete columns 1 (sequential count) and 7 (the "_GSA_CN" column) to use the KKI SNP Analysis Tools to create a WIG file for viewing under UCSC genome browser.]
Do not use the above sample files with the KKI SNP analysis tools, which accept input with fewer columns and analyze data from only one SNP array at a time. Instead, use this 50K sample KKISNP file (in the format needed by KKI SNP Analysis Tools). You can also use this file here to generate a WIG file for custom tracks displayed with the UCSC genome browser. You should be able to visually identify a microdeletion on the 7p arm by looking at the three custom tracks.
Click here for a copy of the WIG file generated by KKI SNP analysis tools from the above sample file. Select this file in the UCSC Genome Browser after clicked on the "add your own customer tracks" button to browse the microceletion on the p arm of chromosome 7. View a screen capture of this output here.
|Download/view the source code|
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Last updated: October 24, 2005.