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lab_1 [2017/04/13 10:29] 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 ====== | ||
+ | |||
+ | |||
+ | ### 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 | ||
+ | ### | ||
+ | |||
+ | |||
+ | ### Question 1 (4 points) | ||
+ | ### a) What does " | ||
+ | |||
+ | |||
+ | ### 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. | ||
+ | |||
+ | ### 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! | ||
+ | |||
+ | ### 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 ' | ||
+ | |||
+ | ### 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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- | ====== | + | ====== |
- | + | ||
- | < | + | |
- | - | + | |
- | - 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 | + | |
- | - genotypes from hu916767_20170324191934.txt | + | |
- | + | ||
- | - | + | |
- | - a) What does " | + | |
- | - | ||
- | - a) Provide a command that I can run to extract only the chromosome column of the genotype file. | ||
- | - | + | **Geography of Genetic Variants Browser** Interactively browse geographic distribution |
- | - a) Provide a command that I can run that extracts only the chromosome column | + | |
- | - b) Provide the output of that command and tell me in your own words what the command did. | + | |
- | - | + | **dbSNP** A fairly exhaustive database of SNPs in humans. https:// |
- | - a) Give me a command that I can run that will extract the most | + | |
- | - | + | |
- | - b) Interpret this individual' | + | |
- | - | + | |
- | - | + | |
- | - Note: you will need to use your web searching abilities! | + | |
- | - | + | **ExAC** A good source for exonic variants. Very user friendly. http:// |
- | - 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? | + | |