Population Genomics Course - Revision history

imported>Weigang: /* Part 3. Estimation of recombination rate */

2013-06-24T04:54:51Z

Part 3. Estimation of recombination rate

← Older revision		Revision as of 04:54, 24 June 2013
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	*In-class exercise: 2-3		*In-class exercise: 2-3
	*Data set: three pairs of sister-group cp26 plasmids		*Data set: three pairs of sister-group cp26 plasmids
			#MUGSY visualization
	*LDhat: [http://ldhat.sourceforge.net/instructions.shtml Instructions]; [http://ldhat.sourceforge.net/manual.pdf PDF Manual]; Based on the "Four-Gamete Test" by [http://www.genetics.org/content/111/1/147.full.pdf+html Hudson & Kaplan, 1985]		*LDhat: [http://ldhat.sourceforge.net/instructions.shtml Instructions]; [http://ldhat.sourceforge.net/manual.pdf PDF Manual]; Based on the "Four-Gamete Test" by [http://www.genetics.org/content/111/1/147.full.pdf+html Hudson & Kaplan, 1985]
	#Download and Install: <~~pre~~ pre style="white-space: pre-wrap;">svn checkout https://ldhat.svn.sourceforge.net/svnroot/ldhat; make; make clean</pre>		#Download and Install: <pre style="white-space: pre-wrap;">svn checkout https://ldhat.svn.sourceforge.net/svnroot/ldhat; make; make clean</pre>
	#Data: cp26.ss.fas		#Data: cp26.ss.fas
	#Convert to LDhat file format: <~~pre~~ pre style="white-space: pre-wrap;">../ldhat/convert -seq cp26.ss.fas -2only -prefix cp26</pre>		#Convert to LDhat file format: <pre style="white-space: pre-wrap;">../ldhat/convert -seq cp26.ss.fas -2only -prefix cp26</pre>
	#Generate likelihood lookup table: <~~pre~~ pre style="white-space: pre-wrap;">../ldhat/lkgen -lk lk_n100_t0.01 -nseq 14; mv new_lk.txt lk_n14_t0.01</pre>		#Generate likelihood lookup table: <pre style="white-space: pre-wrap;">../ldhat/lkgen -lk lk_n100_t0.01 -nseq 14; mv new_lk.txt lk_n14_t0.01</pre>
	#In RStudio: <pre pre style="white-space: pre-wrap;">source("http://ldhat.sourceforge.net/R/coalescent.r")</pre>		#Estimate recombination rates: <pre style="white-space:pre-wrap;">../ldhat/pairwise -lk lk_n14_t0.01 -seq cp26sites.txt -loc cp26locs.txt</pre>
			#Identify hotspots: <pre style="white-space:pre-wrap;">../ldhat/interval -lk lk_n14_t0.01 -seq cp26sites.txt -loc cp26locs.txt</pre>
	*Own script for sister-group counts? (D statistics)		#Summarize results:<pre style="white-space:pre-wrap;">../ldhat/stat -input bounds.txt -burn 500 -loc cp26locs.txt</pre>
			#Visualize in RStudio
			##<pre pre style="white-space: pre-wrap;">source("http://ldhat.sourceforge.net/R/coalescent.r")</pre>
			##Plot "outfile.txt"
			##Plot "fit.txt"
			##Plot "res.txt"

	===Part 4. Simulation of natural selection & Summary===		===Part 4. Simulation of natural selection & Summary===

imported>Weigang: /* Part 3. Estimation of recombination rate */

2013-06-24T03:46:41Z

Part 3. Estimation of recombination rate

← Older revision		Revision as of 03:46, 24 June 2013
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	*In-class exercise: 2-3		*In-class exercise: 2-3
	*Data set: three pairs of sister-group cp26 plasmids		*Data set: three pairs of sister-group cp26 plasmids
	*LDhat: [http://ldhat.sourceforge.net/instructions.shtml Instructions]; [http://ldhat.sourceforge.net/manual.pdf PDF Manual]		*LDhat: [http://ldhat.sourceforge.net/instructions.shtml Instructions]; [http://ldhat.sourceforge.net/manual.pdf PDF Manual]; Based on the "Four-Gamete Test" by [http://www.genetics.org/content/111/1/147.full.pdf+html Hudson & Kaplan, 1985]
	#Download and Install: <pre pre style="white-space: pre-wrap;">svn checkout https://ldhat.svn.sourceforge.net/svnroot/ldhat; make; make clean</pre>		#Download and Install: <pre pre style="white-space: pre-wrap;">svn checkout https://ldhat.svn.sourceforge.net/svnroot/ldhat; make; make clean</pre>
	#Data: cp26.ss.fas		#Data: cp26.ss.fas

imported>Weigang: /* Part 3. Estimation of recombination rate */

2013-06-23T18:38:49Z

Part 3. Estimation of recombination rate

← Older revision		Revision as of 18:38, 23 June 2013
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	#Data: cp26.ss.fas		#Data: cp26.ss.fas
	#Convert to LDhat file format: <pre pre style="white-space: pre-wrap;">../ldhat/convert -seq cp26.ss.fas -2only -prefix cp26</pre>		#Convert to LDhat file format: <pre pre style="white-space: pre-wrap;">../ldhat/convert -seq cp26.ss.fas -2only -prefix cp26</pre>
			#Generate likelihood lookup table: <pre pre style="white-space: pre-wrap;">../ldhat/lkgen -lk lk_n100_t0.01 -nseq 14; mv new_lk.txt lk_n14_t0.01</pre>
	#In RStudio: <pre pre style="white-space: pre-wrap;">source("http://ldhat.sourceforge.net/R/coalescent.r")</pre>		#In RStudio: <pre pre style="white-space: pre-wrap;">source("http://ldhat.sourceforge.net/R/coalescent.r")</pre>

imported>Weigang: /* Part 3. Estimation of recombination rate */

2013-06-23T18:22:58Z

Part 3. Estimation of recombination rate

← Older revision		Revision as of 18:22, 23 June 2013
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	*In-class exercise: 2-3		*In-class exercise: 2-3
	*Data set: three pairs of sister-group cp26 plasmids		*Data set: three pairs of sister-group cp26 plasmids
	*LDhat: [http://sourceforge.net/~~projects~~/ldhat/ ~~Source & Docs~~]		*LDhat: [http://ldhat.sourceforge.net/instructions.shtml Instructions]; [http://ldhat.sourceforge.net/manual.pdf PDF Manual]
	#Download and Install: <pre pre style="white-space: pre-wrap;">svn checkout https://ldhat.svn.sourceforge.net/svnroot/ldhat; make; make clean</pre>		#Download and Install: <pre pre style="white-space: pre-wrap;">svn checkout https://ldhat.svn.sourceforge.net/svnroot/ldhat; make; make clean</pre>
			#Data: cp26.ss.fas
			#Convert to LDhat file format: <pre pre style="white-space: pre-wrap;">../ldhat/convert -seq cp26.ss.fas -2only -prefix cp26</pre>
			#In RStudio: <pre pre style="white-space: pre-wrap;">source("http://ldhat.sourceforge.net/R/coalescent.r")</pre>

	*Own script for sister-group counts? (D statistics)		*Own script for sister-group counts? (D statistics)

imported>Weigang: /* Part 3. Estimation of recombination rate */

2013-06-23T17:42:04Z

Part 3. Estimation of recombination rate

← Older revision		Revision as of 17:42, 23 June 2013
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	*In-class exercise: 2-3		*In-class exercise: 2-3
	*Data set: three pairs of sister-group cp26 plasmids		*Data set: three pairs of sister-group cp26 plasmids
	*LDhat [http://sourceforge.net/projects/ldhat/]		*LDhat: [http://sourceforge.net/projects/ldhat/ Source & Docs]
	#Download and Install: <pre pre style="white-space: pre-wrap;">svn checkout https://ldhat.svn.sourceforge.net/svnroot/ldhat; make; make clean</pre>		#Download and Install: <pre pre style="white-space: pre-wrap;">svn checkout https://ldhat.svn.sourceforge.net/svnroot/ldhat; make; make clean</pre>

imported>Weigang: /* Part 3. Estimation of recombination rate */

2013-06-23T17:41:18Z

Part 3. Estimation of recombination rate

← Older revision		Revision as of 17:41, 23 June 2013
Line 31:		Line 31:
	*In-class exercise: 2-3		*In-class exercise: 2-3
	*Data set: three pairs of sister-group cp26 plasmids		*Data set: three pairs of sister-group cp26 plasmids
	*LDhat		*LDhat [http://sourceforge.net/projects/ldhat/]
	#Download and Install: <pre pre style="white-space: pre-wrap;">svn checkout https://ldhat.svn.sourceforge.net/svnroot/ldhat; make; make clean</pre>		#Download and Install: <pre pre style="white-space: pre-wrap;">svn checkout https://ldhat.svn.sourceforge.net/svnroot/ldhat; make; make clean</pre>

imported>Weigang: /* Part 3. Estimation of recombination rate */

2013-06-23T17:39:46Z

Part 3. Estimation of recombination rate

← Older revision		Revision as of 17:39, 23 June 2013
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	*In-class exercise: 2-3		*In-class exercise: 2-3
	*Data set: three pairs of sister-group cp26 plasmids		*Data set: three pairs of sister-group cp26 plasmids
	*~~LAMAC~~; ~~LDhat~~		*LDhat
			#Download and Install: <pre pre style="white-space: pre-wrap;">svn checkout https://ldhat.svn.sourceforge.net/svnroot/ldhat; make; make clean</pre>

	*Own script for sister-group counts? (D statistics)		*Own script for sister-group counts? (D statistics)

	===Part 4. Simulation of natural selection & Summary===		===Part 4. Simulation of natural selection & Summary===
	*In-class exercise: 3:30-5		*In-class exercise: 3:30-5

imported>Weigang: /* Part 1. Introduction & Overview */

2013-06-19T05:52:44Z

Part 1. Introduction & Overview

← Older revision		Revision as of 05:52, 19 June 2013
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	** Recombination: Muller's Rachet; Hill-Roberson effect		** Recombination: Muller's Rachet; Hill-Roberson effect
	** Recombination and natural selection: Background selection & selective sweeps		** Recombination and natural selection: Background selection & selective sweeps
	*~~Bacterial population structure~~: B. burgdorferi in Northeast US		*Applications
			** GWAS
			** Population history: phylogeny, structuring, gene flow, and selective sweeps (e.g., Neandertal genomes; Borrelia burgdorferi in Northeast US)
			** Genomic surveillance of infectious diseases
	*Bioinformatics pipeline/protocol		*Bioinformatics pipeline/protocol
	*In-Class Exercise ~~(15 min)~~: ~~Tree Puzzles~~		*In-Class Exercise: Software setup & data download

	===Part 2. Building genome phylogeny/Geographic structuring/Population growth?===		===Part 2. Building genome phylogeny/Geographic structuring/Population growth?===
	*In-class exercise: 10:00-11:30		*In-class exercise: 10:00-11:30

imported>Weigang: /* Part 2. Building genome phylogeny/Geographic structuring/Population growth? */

2013-05-31T18:19:12Z

Part 2. Building genome phylogeny/Geographic structuring/Population growth?

← Older revision		Revision as of 18:19, 31 May 2013
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	*Genome alignment: MUGSY & Alignment viewer: Gmaj		*Genome alignment: MUGSY & Alignment viewer: Gmaj
	*Genome tree: FastTree		*Genome tree: FastTree
	*Tree ~~viewer~~: R package APE		*Tree re-rooting: R package APE [http://borreliagenome.org/wiki/Biol425_2013#May_1:_Molecular_Phylogenetics_.28Part_2.29 see syllabus]
			*Interactive tree viewer: [http://www.trex.uqam.ca/index.php?action=newick&project=trex trexonline]

	===Part 3. Estimation of recombination rate===		===Part 3. Estimation of recombination rate===
	*In-class exercise: 2-3		*In-class exercise: 2-3

imported>Weigang: /* Syllabus */

2013-05-26T15:06:34Z

Syllabus

← Older revision		Revision as of 15:06, 26 May 2013
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	==Syllabus==		==Syllabus==
	===Part 1. Introduction & Overview===		===Part 1. Introduction & Overview===
	• Lecture ~~(45 min)~~		*Lecture: 8:30-9:30
	o Bacterial population structure: B. burgdorferi in Northeast US		*Population processes
	~~o Phylogenetic vs. coalescent trees~~		** Recombination: Muller's Rachet; Hill-Roberson effect
	o Bioinformatics pipeline/protocol		** Recombination and natural selection: Background selection & selective sweeps
	• In-Class Exercise (15 min): Tree Puzzles		*Bacterial population structure: B. burgdorferi in Northeast US
			*Bioinformatics pipeline/protocol
			*In-Class Exercise (15 min): Tree Puzzles
	===Part 2. Building genome phylogeny/Geographic structuring/Population growth?===		===Part 2. Building genome phylogeny/Geographic structuring/Population growth?===
	• Data: cp26 plasmids from ~~~20~~ B. burgdorferi sensu lato genomes		*In-class exercise: 10:00-11:30
	~~• Demo (15 min)~~		*Data set: cp26 plasmids from 23 B. burgdorferi sensu lato genomes
	o Genome alignment: MUGSY		*Genome alignment: MUGSY & Alignment viewer: Gmaj
	o Alignment viewer: Gmaj		*Genome tree: FastTree
	o Genome tree: FastTree		*Tree viewer: R package APE
	o Tree viewer: R package APE
	~~• In-Class Exercise (45 min)~~
	===Part 3. Estimation of recombination rate===		===Part 3. Estimation of recombination rate===
	• Data: three pairs of sister-group cp26 plasmids		*In-class exercise: 2-3
	~~• Demo (15 min):~~		*Data set: three pairs of sister-group cp26 plasmids
	o LAMAC		*LAMAC; LDhat
	o LDhat		*Own script for sister-group counts? (D statistics)
	o Own script for sister-group counts?
	~~• In-Class Exercise~~ (~~45 min~~)
	===Part 4. Simulation of natural selection & Summary===		===Part 4. Simulation of natural selection & Summary===
	~~• Data~~:		*In-class exercise: 3:30-5
	~~• Demo (20 min):~~ BacSim		*ms, seq-gen; Genomes
	~~• In-Class Exercise (45 min):~~		*BacSim

	==Assignment & Assessment==		==Assignment & Assessment==