This shows you the differences between two versions of the page.
Both sides previous revision Previous revision Next revision | Previous revision Last revision Both sides next revision | ||
lab_1 [2017/04/11 14:12] scott |
lab_1 [2017/04/13 13:43] scott /* Example commands */ |
||
---|---|---|---|
Line 1: | Line 1: | ||
+ | |||
+ | ====== Genotype file ====== | ||
+ | |||
+ | The genotype file is located here: https:// | ||
+ | |||
+ | |||
+ | ====== 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 | ||
+ | |||
+ | |||
+ | |||
+ | ====== Example commands ====== | ||
+ | |||
+ | |||
### PSYCH 3102 Behavioral Genetics | ### PSYCH 3102 Behavioral Genetics | ||
Line 110: | Line 161: | ||
### 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 ' | ||
+ | |||
Line 143: | Line 200: | ||
### this command going to work? Why or why not? | ### this command going to work? Why or why not? | ||
grep -E ' | grep -E ' | ||
+ | |||
+ | |||
+ | |||
+ | ====== Useful databases ====== | ||
+ | |||
+ | |||
+ | **Geography of Genetic Variants Browser** Interactively browse geographic distribution of genetic variants. Can compare to 1000 Genomes, ExAC, and POPRES (Euro-centric). http:// | ||
+ | |||
+ | **dbSNP** A fairly exhaustive database of SNPs in humans. https:// | ||
+ | |||
+ | **ExAC** A good source for exonic variants. Very user friendly. http:// | ||