Biol425 2015 - Revision history

imported>Weigang: /* Useful Links */

2016-01-25T20:20:07Z

Useful Links

← Older revision		Revision as of 20:20, 25 January 2016
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	==Useful Links==		==Useful Links==
			* [http://korflab.ucdavis.edu/Unix_and_Perl/current.html An online UNIX & PERL Tutorial for biologiests]

	===Unix Tutorials===		===Unix Tutorials===

2015-05-13T14:21:13Z

April 29: Population Analysis (1)

← Older revision		Revision as of 14:21, 13 May 2015
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	$is_snp{$pos} = 0;		$is_snp{$pos} = 0;
	}		}
			}

	# Part III. Print haplotypes (i.e., nucleotides at SNP sites for each chromosome)		# Part III. Print haplotypes (i.e., nucleotides at SNP sites for each chromosome)

2015-05-13T14:20:42Z

April 29: Population Analysis (1)

← Older revision		Revision as of 14:20, 13 May 2015
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	print $id, "\t";		print $id, "\t";
	for (my $pos = 0; $pos < $length; $pos++) { # for each site		for (my $pos = 0; $pos < $length; $pos++) { # for each site
	next unless is_snp{$pos}; # skip constant site		next unless $is_snp{$pos}; # skip constant site
	print $seqs{$id}->[$pos]; # print nt at a SNP site		print $seqs{$id}->[$pos]; # print nt at a SNP site
	}		}

2015-05-13T14:20:17Z

April 29: Population Analysis (1)

← Older revision		Revision as of 14:20, 13 May 2015
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	print $id, "\t";		print $id, "\t";
	for (my $pos = 0; $pos < $length; $pos++) { # for each site		for (my $pos = 0; $pos < $length; $pos++) { # for each site
	next unless ?; # skip constant site		next unless is_snp{$pos}; # skip constant site
	print ?; # print nt at a SNP site		print $seqs{$id}->[$pos]; # print nt at a SNP site
	}		}
	print "\n";		print "\n";

2015-05-13T14:00:01Z

May 13: Final Review

← Older revision		Revision as of 14:00, 13 May 2015
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	===May 13: Final Review===		===May 13: Final Review===
	* Review slides: [[File: Final-~~review~~-~~slides~~.pdf\|thumbnail]]		* Review slides: [[File: Final-Review-small-bio425-sp-2015.pdf\|thumbnail]]
	* Tutorial 3. Database access with DBI		* Tutorial 3. Database access with DBI
	* [http://www.hunter.cuny.edu/te '''Teacher's evaluation''']		* [http://www.hunter.cuny.edu/te '''Teacher's evaluation''']

2015-05-13T13:05:14Z

May 13: Final Review

← Older revision		Revision as of 13:05, 13 May 2015
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	===May 13: Final Review===		===May 13: Final Review===
	* Review slides: [[File:Final-review-~~small~~.pdf\|thumbnail]]		* Review slides: [[File: Final-review-slides.pdf\|thumbnail]]
	* Tutorial 3. Database access with DBI		* Tutorial 3. Database access with DBI
	* [http://www.hunter.cuny.edu/te '''Teacher's evaluation''']		* [http://www.hunter.cuny.edu/te '''Teacher's evaluation''']

2015-05-13T13:04:05Z

May 13: Final Review

← Older revision		Revision as of 13:04, 13 May 2015
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	===May 13: Final Review===		===May 13: Final Review===
			* Review slides: [[File:Final-review-small.pdf\|thumbnail]]
	* Tutorial 3. Database access with DBI		* Tutorial 3. Database access with DBI
	* [http://www.hunter.cuny.edu/te '''Teacher's evaluation''']		* [http://www.hunter.cuny.edu/te '''Teacher's evaluation''']

2015-05-06T21:17:34Z

May 6: Population Analysis (2)

← Older revision		Revision as of 21:17, 6 May 2015
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	* Tutorial 1. Test linkage disequilibrium (LD)		* Tutorial 1. Test linkage disequilibrium (LD)
	* Tutorial 2. Genome-wide association studies (GWAS)		* Tutorial 2. Genome-wide association studies (GWAS)
			* Tutorial 3. Test of Hardy-Weinberg equilibrium (for random mating & presence of natural selection)

	===May 13: Final Review===		===May 13: Final Review===

2015-05-06T21:02:59Z

May 13: Final Review

← Older revision		Revision as of 21:02, 6 May 2015
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	===May 13: Final Review===		===May 13: Final Review===
			* Tutorial 3. Database access with DBI
	* [http://www.hunter.cuny.edu/te '''Teacher's evaluation''']		* [http://www.hunter.cuny.edu/te '''Teacher's evaluation''']
			* All make-up assignments due May 20.

	===May 20: Final Exam===		===May 20: Final Exam===

2015-05-06T21:01:58Z

May 6: Population Analysis (2)

← Older revision		Revision as of 21:01, 6 May 2015
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	* Tutorial 1. Test linkage disequilibrium (LD)		* Tutorial 1. Test linkage disequilibrium (LD)
	* Tutorial 2. Genome-wide association studies (GWAS)		* Tutorial 2. Genome-wide association studies (GWAS)
	* Tutorial 3. Database access with DBI

	===May 13: Final Review===		===May 13: Final Review===