lab_1
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lab_1 [2017/04/11 14:14] scott |
lab_1 [2017/04/13 13:43] scott /* Example commands */ |
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| The genotype file is located here: https:// | The genotype file is located here: https:// | ||
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| + | ====== Lab 1 Assignment ====== | ||
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| + | ### Lab 1 assignment | ||
| + | ### Assigned: 4/13/2017 | ||
| + | ### Due: 4/20/2017 at the beginning of class. Late assignments (even by 5 minutes) | ||
| + | ### will not be accepted! | ||
| + | ### | ||
| + | ### Note: all questions should be answered with respect to the | ||
| + | ### | ||
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| + | ### Question 1 (4 points) | ||
| + | ### a) What does " | ||
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| + | ### Question 2 (2 points) | ||
| + | ### a) Provide a command that I can run to extract only the chromosome column of the genotype file. | ||
| + | |||
| + | ### Question 3 (2 points) | ||
| + | ### a) Provide a command that I can run that extracts only the chromosome column of the genotype | ||
| + | ### file, and pipes it to "sort -u". | ||
| + | ### b) Provide the output of that command and tell me in your own words what the command did. | ||
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| + | ### Question 4 (6 points) | ||
| + | ### a) Give me a command that I can run that will extract the most | ||
| + | ### commonly studied SNP associated with the flushing response discussed in class. | ||
| + | ### b) Interpret this individual' | ||
| + | ### esophageal cancer, and their response to Disulfiram. | ||
| + | ### | ||
| + | ### Note: you will need to use your web searching abilities! | ||
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| + | ### Question 5 (4 points) | ||
| + | ### Find out more about SNP rs72921001 in dbSNP | ||
| + | ### a) What is the minor allele in individuals of European ancestry? What is the MAF? | ||
| + | ### b) What is the allele frequency of this allele in individuals of African ancestry? | ||
| + | ### c) Is this SNP associated with any phenotypic effects? | ||
| + | ### d) Describe the geographical distribution of allele frequency for this variant using | ||
| + | ### the website | ||
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| ### We can also grab both variants, if we wanted to | ### We can also grab both variants, if we wanted to | ||
| grep -E ' | grep -E ' | ||
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| + | ### What if we have a variant where we don't know the rsID, | ||
| + | ### but only the chromosome, position, genome build, and alleles? | ||
| + | ### Well, to get chromosome 1, position 11850759, we can do this: | ||
| + | grep -E ' | ||
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| grep -E ' | grep -E ' | ||
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| + | ====== Useful databases ====== | ||
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| + | **Geography of Genetic Variants Browser** Interactively browse geographic distribution of genetic variants. Can compare to 1000 Genomes, ExAC, and POPRES (Euro-centric). http:// | ||
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| + | **dbSNP** A fairly exhaustive database of SNPs in humans. https:// | ||
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| + | **ExAC** A good source for exonic variants. Very user friendly. http:// | ||
lab_1.txt · Last modified: 2017/04/25 10:49 by scott
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