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lab_1 [2017/04/13 10:32] scott |
lab_1 [2017/04/25 10:49] (current) scott /* Lab 1 Assignment */ |
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### Question 1 (4 points) | ### Question 1 (4 points) | ||
### a) What does " | ### a) What does " | ||
- | |||
### Question 2 (2 points) | ### Question 2 (2 points) | ||
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### b) What is the allele frequency of this allele in individuals of African ancestry? | ### b) What is the allele frequency of this allele in individuals of African ancestry? | ||
### c) Is this SNP associated with any phenotypic effects? | ### c) Is this SNP associated with any phenotypic effects? | ||
+ | ### d) Describe the geographical distribution of allele frequency for this variant using | ||
+ | ### the website | ||
+ | |||
+ | Example full credit answers: | ||
+ | - Question 1 | ||
+ | - "The positive strand refers to the leading strand of DNA being sequenced (eg. the strand that RNA would be replicated against)." | ||
+ | - "Each DNA strand is a double helix - it has two strands. The first strand given is the postive strand; the second strand is based on the first and is called the negative strand. For example, if the positive strand is ATCGG, then the negative strand is TAGCC (T always pairs with A, and G always pairs with C). The header is stating that the genome provided is only based on the first strand (the positive strand)." | ||
+ | - Question 2 | ||
+ | - awk ' | ||
+ | - cut -f2 hu916767_20170324191934.txt | ||
+ | - Question 3 | ||
+ | - awk ' | ||
+ | - cut -f2 hu916767_20170324191934.txt | sort -u | ||
+ | - The command extracts the second column from a tab-delimited file, alphanumerically sorts it, and removes all duplicate lines. | ||
+ | - Question 4 | ||
+ | - grep ' | ||
+ | - Output: rs671 12 112241766 GG | ||
+ | - " | ||
+ | - Question 5 | ||
+ | - Minor allele is A in individuals of European ancestry and MAF is .36 | ||
+ | - In individuals of African ancestry MAF is .021 | ||
+ | - The SNP is associated with thinking cilantro tastes like soap | ||
+ | - "The minor allele is most common in central/ | ||
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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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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:// | ||