NgsAdmixTutorial - Revision history

Thorfinn: /* The output */

2022-06-06T22:59:21Z

The output

← Older revision		Revision as of 00:59, 7 June 2022
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	::<code>head -n 5 Demo1NGSadmix.qopt</code>		::<code>head -n 5 Demo1NGSadmix.qopt</code>

	~~#*'''DemoNGSadmix.filter''' if the filter was used, it will show the sites that were left out.~~
	#
	~~#::To see the header file, type:~~
	#
	~~#::<code>head -n 5 $OUT_DIR/Demo1NGSadmix.filter</code>~~
	#
	~~#::no lines means that all where used~~

	=== Plot the results in R ===		=== Plot the results in R ===

Thorfinn: /* The output */

2022-06-06T22:59:03Z

The output

← Older revision		Revision as of 00:59, 7 June 2022
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	::<code>head -n 5 Demo1NGSadmix.qopt</code>		::<code>head -n 5 Demo1NGSadmix.qopt</code>

	*'''DemoNGSadmix.filter''' if the filter was used, it will show the sites that were left out.		#*'''DemoNGSadmix.filter''' if the filter was used, it will show the sites that were left out.
			#
	::To see the header file, type:		#::To see the header file, type:
			#
	::<code>head -n 5 $OUT_DIR/Demo1NGSadmix.filter</code>		#::<code>head -n 5 $OUT_DIR/Demo1NGSadmix.filter</code>
			#
	::no lines means that all where used		#::no lines means that all where used

	=== Plot the results in R ===		=== Plot the results in R ===

Thorfinn: /* The test data */

2022-06-06T22:55:35Z

The test data

← Older revision		Revision as of 00:55, 7 June 2022
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	You can either download the beagle input files or create them yourself from bam files		You can either download the beagle input files or create them yourself from bam files. Therefore you should choose either 'Download the beagle genotype likelihood input file' or 'Create the the beagle genotype likelihood input file using ANGSD'.
	====Download the beagle genotype likelihood input file====		====Download the beagle genotype likelihood input file====
	NGSadmix uses Genotype Likelihoods (GLs) in .beagle format as input. The input file has been created for you.		NGSadmix uses Genotype Likelihoods (GLs) in .beagle format as input. The input file has been created for you.

Thorfinn: /* Create directories */

2022-06-06T22:49:51Z

Create directories

← Older revision		Revision as of 00:49, 7 June 2022
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	<code>mkdir Results</code>		<code>mkdir Results</code>

			<code>cd ..</code>

	===Set the paths to your local directories===		===Set the paths to your local directories===

Thorfinn at 03:18, 2 May 2020

2020-05-02T03:18:26Z

← Older revision		Revision as of 05:18, 2 May 2020
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	We will go through a simple and more complex example on how to use NGSadmix with visualization of the data.		We will go through a simple and more complex example on how to use NGSadmix with visualization of the data.

			User need to to add -printInfo 1 in order to get information about sites retained for analysis.

	==Example of NGSadmix - very small data set==		==Example of NGSadmix - very small data set==

Sonia4: /* Run NGSadmix */

2019-07-29T22:03:48Z

Run NGSadmix

← Older revision		Revision as of 00:03, 30 July 2019
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	===Run NGSadmix===		===Run NGSadmix===
	Run an analysis of the data with NGSadmix with K=3 (-K 3), using 1 cpu (-P 1), using only SNPs with minor allele frequency above 0.05 (-minMaf 0.05), set the seed set to 21 (-seed 21), and set the prefix of the output files to Demo2NGSadmixK3. For a reference on the parameters that can be used to run NGSadmix, please go to [http://www.popgen.dk/software/index.php/NgsAdmixv2#Parameters]		Run an analysis of the data with NGSadmix with K=3 (-K 3), using 1 cpu (-P 1), using only SNPs with minor allele frequency above 0.05 (-minMaf 0.05), set the seed set to 21 (-seed 21), and set the prefix of the output files to Demo2NGSadmixK3. For a reference on the parameters that can be used to run NGSadmix, please go to [http://www.popgen.dk/software/index.php/NgsAdmixv2#Parameters]


	<code>$NGSADMIX -likes $IN_DIR/Demo2input.gz -K 3 -P 1 -minMaf 0.05 -seed 21 -o $OUT_DIR/Demo2NGSadmixK3</code>		<code>$NGSADMIX -likes $IN_DIR/Demo2input.gz -K 3 -P 1 -minMaf 0.05 -seed 21 -o $OUT_DIR/Demo2NGSadmixK3</code>

Sonia4: /* Download */

2019-07-29T22:03:38Z

Download

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	''Note: please make sure you have created and set up the working directories as indicated in the previous tutorial.''		''Note: please make sure you have created and set up the working directories as indicated in the previous tutorial.''

	===Download===		===Download Files===
	Download and copy the files to your input folder (for example, $IN_DIR)		Download and copy the files to your input folder (for example, $IN_DIR)
	<pre>		<pre>

Sonia4: /* Plot the results in R */

2019-07-29T22:03:18Z

Plot the results in R

← Older revision		Revision as of 00:03, 30 July 2019
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	barplot(t(q)[,ord],col=c(2,1,3),names=pop[ord],las=2,ylab="Demo1 Admixture proportions",cex.names=0.75)		barplot(t(q)[,ord],col=c(2,1,3),names=pop[ord],las=2,ylab="Demo1 Admixture proportions",cex.names=0.75)
	</pre>		</pre>


	The y-axis of the plot show the admixture proportions and the individuals in the samples are plotted in the x-axis.		The y-axis of the plot show the admixture proportions and the individuals in the samples are plotted in the x-axis.

Sonia4: /* Plot the results in R */

2019-07-29T22:03:02Z

Plot the results in R

← Older revision		Revision as of 00:03, 30 July 2019
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	<code>cd $OUT_DIR</code>		<code>cd $OUT_DIR</code>

	::Type “R” in the terminal and press enter and paste the following code into R:		Type “R” in the terminal and press enter and paste the following code into R:

	<pre>		<pre>

Sonia4: /* The output */

2019-07-29T22:02:38Z

The output

← Older revision		Revision as of 00:02, 30 July 2019
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	*'''Estimated allele frequency'''		*'''Estimated allele frequency'''

	A zipped .fopt file, that contains an estimate of the allele frequency in each of the 3 assumed ancestral populations (there is a line for each locus).		::A zipped .fopt file, that contains an estimate of the allele frequency in each of the 3 assumed ancestral populations (there is a line for each locus).

	We can use this file to obtain the estimated allele frequency of the first 5 SNPs (one per line) of the three assumed ancestral populations, by typing the following command:		::We can use this file to obtain the estimated allele frequency of the first 5 SNPs (one per line) of the three assumed ancestral populations, by typing the following command:

	<code>zcat $OUT_DIR/Demo1NGSadmix.fopt.gz \| head -n 5</code>		::<code>zcat $OUT_DIR/Demo1NGSadmix.fopt.gz \| head -n 5</code>

	*'''Estimated admixture proportions'''		*'''Estimated admixture proportions'''
	A .qopt file, that contains an estimate of the individual's ancestry proportion from each of the three assumed ancestral populations (there is a line for each individual).		::A .qopt file, that contains an estimate of the individual's ancestry proportion from each of the three assumed ancestral populations (there is a line for each individual).

	To obtain the estimated admixture proportions for the first 5 individuals, type the following command:		::To obtain the estimated admixture proportions for the first 5 individuals, type the following command:

	<code>head -n 5 Demo1NGSadmix.qopt</code>		::<code>head -n 5 Demo1NGSadmix.qopt</code>

	*'''DemoNGSadmix.filter''' if the filter was used, it will show the sites that were left out.		*'''DemoNGSadmix.filter''' if the filter was used, it will show the sites that were left out.

	To see the header file, type:		::To see the header file, type:

	<code>head -n 5 $OUT_DIR/Demo1NGSadmix.filter</code>		::<code>head -n 5 $OUT_DIR/Demo1NGSadmix.filter</code>

	no lines means that all where used		::no lines means that all where used

	=== Plot the results in R ===		=== Plot the results in R ===