Tutorial - Revision history

>Admin at 19:23, 5 August 2019

2019-08-05T19:23:15Z

← Older revision		Revision as of 19:23, 5 August 2019
Line 67:		Line 67:

	<code>		<code>
	CACCTGGTGG 5.133463 ~~<br/>~~		CACCTGGTGG 5.133463
	CACCAGGTGG 5.090566 ~~<br/>~~		CACCAGGTGG 5.090566
	CACCAGGGGG 5.038873 ~~<br/>~~		CACCAGGGGG 5.038873
	CCACTAGGGG 4.833398 ~~<br/>~~		CCACTAGGGG 4.833398
	CCACCAGGGG 4.832404 ~~<br/>~~		CCACCAGGGG 4.832404
	CACCTAGTGG 4.782613 ~~<br/>~~		CACCTAGTGG 4.782613
	CACCAGAGGG 4.707206 ~~<br/>~~		CACCAGAGGG 4.707206
	CACTAGGGGG 4.663015 ~~<br/>~~		CACTAGGGGG 4.663015
	CACTAGAGGG 4.610800 ~~<br/>~~		CACTAGAGGG 4.610800
	CACTAGGTGG 4.580834		CACTAGGTGG 4.580834
	CCACTAGAGG 4.529869		CCACTAGAGG 4.529869
	CAGCAGAGGG 4.335304		CAGCAGAGGG 4.335304
			...
	</code>		</code>

>Admin at 19:22, 5 August 2019

2019-08-05T19:22:22Z

← Older revision		Revision as of 19:22, 5 August 2019
Line 67:		Line 67:

	<code>		<code>
	CACCTGGTGG 5.133463 <br/>		CACCTGGTGG 5.133463 <br/>
	CACCAGGTGG 5.090566 <br/>		CACCAGGTGG 5.090566 <br/>
	CACCAGGGGG 5.038873 <br/>		CACCAGGGGG 5.038873 <br/>
	CCACTAGGGG 4.833398 <br/>		CCACTAGGGG 4.833398 <br/>
	CCACCAGGGG 4.832404 <br/>		CCACCAGGGG 4.832404 <br/>
	CACCTAGTGG 4.782613 <br/>		CACCTAGTGG 4.782613 <br/>
	CACCAGAGGG 4.707206 <br/>		CACCAGAGGG 4.707206 <br/>
	CACTAGGGGG 4.663015 <br/>		CACTAGGGGG 4.663015 <br/>
	CACTAGAGGG 4.610800 <br/>		CACTAGAGGG 4.610800 <br/>
	CACTAGGTGG 4.580834		CACTAGGTGG 4.580834
	CCACTAGAGG 4.529869		CCACTAGAGG 4.529869
	CAGCAGAGGG 4.335304		CAGCAGAGGG 4.335304
	</code>		</code>

>Admin at 19:19, 5 August 2019

2019-08-05T19:19:59Z

← Older revision		Revision as of 19:19, 5 August 2019
Line 76:		Line 76:
	CACTAGGGGG 4.663015 <br/>		CACTAGGGGG 4.663015 <br/>
	CACTAGAGGG 4.610800 <br/>		CACTAGAGGG 4.610800 <br/>
	CACTAGGTGG 4.580834 ~~<br/>~~		CACTAGGTGG 4.580834
	CCACTAGAGG 4.529869 ~~<br/>~~		CCACTAGAGG 4.529869
	CAGCAGAGGG 4.335304 ~~<br/>~~		CAGCAGAGGG 4.335304
	</code>		</code>

>Admin at 19:19, 5 August 2019

2019-08-05T19:19:30Z

← Older revision		Revision as of 19:19, 5 August 2019
Line 66:		Line 66:
	which should give weights very similar to:		which should give weights very similar to:

	<~~span style="font-family:Courier"~~>		<code>
	CACCTGGTGG 5.133463 <br/>		CACCTGGTGG 5.133463 <br/>
	CACCAGGTGG 5.090566 <br/>		CACCAGGTGG 5.090566 <br/>
Line 79:		Line 79:
	CCACTAGAGG 4.529869 <br/>		CCACTAGAGG 4.529869 <br/>
	CAGCAGAGGG 4.335304 <br/>		CAGCAGAGGG 4.335304 <br/>
	</~~span~~>		</code>

	5. To calculate the impact of a variant, in this case on CTCF binding, we use gkmsvm_classify to find the		5. To calculate the impact of a variant, in this case on CTCF binding, we use gkmsvm_classify to find the

>Admin at 19:12, 5 August 2019

2019-08-05T19:12:07Z

← Older revision		Revision as of 19:12, 5 August 2019
Line 66:		Line 66:
	which should give weights very similar to:		which should give weights very similar to:

	<span style="font-family:Courier;">		<span style="font-family:Courier">
	CACCTGGTGG 5.133463 <br/>		CACCTGGTGG 5.133463 <br/>
	CACCAGGTGG 5.090566 <br/>		CACCAGGTGG 5.090566 <br/>

>Admin at 19:10, 5 August 2019

2019-08-05T19:10:54Z

← Older revision		Revision as of 19:10, 5 August 2019
Line 66:		Line 66:
	which should give weights very similar to:		which should give weights very similar to:

			<span style="font-family:Courier;">
	CACCTGGTGG 5.133463 <br/>		CACCTGGTGG 5.133463 <br/>
	CACCAGGTGG 5.090566 <br/>		CACCAGGTGG 5.090566 <br/>
Line 78:		Line 79:
	CCACTAGAGG 4.529869 <br/>		CCACTAGAGG 4.529869 <br/>
	CAGCAGAGGG 4.335304 <br/>		CAGCAGAGGG 4.335304 <br/>
			</span>

	5. To calculate the impact of a variant, in this case on CTCF binding, we use gkmsvm_classify to find the		5. To calculate the impact of a variant, in this case on CTCF binding, we use gkmsvm_classify to find the

>Admin at 19:06, 5 August 2019

2019-08-05T19:06:14Z

← Older revision		Revision as of 19:06, 5 August 2019
Line 39:		Line 39:

	Now to run gkmSVM-R on the ctcf test set from Ghandi Lee, Mohammad-Noori, Beer, PLOS CompBio 2014:		Now to run gkmSVM-R on the ctcf test set from Ghandi Lee, Mohammad-Noori, Beer, PLOS CompBio 2014:

	~~Input files: ctcfpos.bed nr10mers.fa~~

	Input files: [http://www.beerlab.org/gkmsvm/ctcfpos.bed ctcfpos.bed], [http://www.beerlab.org/gkmsvm/nr10mers.fa nr10mers.fa], [http://www.beerlab.org/gkmsvm/ref.fa ref.fa], [http://www.beerlab.org/gkmsvm/alt.fa alt.fa] from [http://www.beerlab.org/gkmsvm www.beerlab.org/gkmsvm]		Input files: [http://www.beerlab.org/gkmsvm/ctcfpos.bed ctcfpos.bed], [http://www.beerlab.org/gkmsvm/nr10mers.fa nr10mers.fa], [http://www.beerlab.org/gkmsvm/ref.fa ref.fa], [http://www.beerlab.org/gkmsvm/alt.fa alt.fa] from [http://www.beerlab.org/gkmsvm www.beerlab.org/gkmsvm]

>Admin at 19:04, 5 August 2019

2019-08-05T19:04:56Z

← Older revision		Revision as of 19:04, 5 August 2019
Line 40:		Line 40:
	Now to run gkmSVM-R on the ctcf test set from Ghandi Lee, Mohammad-Noori, Beer, PLOS CompBio 2014:		Now to run gkmSVM-R on the ctcf test set from Ghandi Lee, Mohammad-Noori, Beer, PLOS CompBio 2014:

	Input files: ctcfpos.bed nr10mers.fa		Input files: ctcfpos.bed nr10mers.fa

	Input files: [[http://www.beerlab.org/ctcfpos.bed]], [[http://www.beerlab.org/nr10mers.fa]], [[http://www.beerlab.org/ref.fa]], [[http://www.beerlab.org/alt.fa]] from [[http://www.beerlab.org/gkmsvm\|www.beerlab.org/gkmsvm]]		Input files: [http://www.beerlab.org/gkmsvm/ctcfpos.bed ctcfpos.bed], [http://www.beerlab.org/gkmsvm/nr10mers.fa nr10mers.fa], [http://www.beerlab.org/gkmsvm/ref.fa ref.fa], [http://www.beerlab.org/gkmsvm/alt.fa alt.fa] from [http://www.beerlab.org/gkmsvm www.beerlab.org/gkmsvm]

	1. generate GC, length, and repeat matched negative set and extract fasta sequence files for ctcfpos.fa and ctcfneg_1x.fa: (Larger negative sets can be generated by increasing xfold, and running time can be decreased by reducing nMaxTrials, at the cost of not matching difficult sequences. In general training on larger sequence sets will produce more accurate and robust models.)		1. generate GC, length, and repeat matched negative set and extract fasta sequence files for ctcfpos.fa and ctcfneg_1x.fa: (Larger negative sets can be generated by increasing xfold, and running time can be decreased by reducing nMaxTrials, at the cost of not matching difficult sequences. In general training on larger sequence sets will produce more accurate and robust models.)

>Admin at 19:01, 5 August 2019

2019-08-05T19:01:13Z

← Older revision		Revision as of 19:01, 5 August 2019
Line 41:		Line 41:

	Input files: ctcfpos.bed nr10mers.fa		Input files: ctcfpos.bed nr10mers.fa

			Input files: [[http://www.beerlab.org/ctcfpos.bed]], [[http://www.beerlab.org/nr10mers.fa]], [[http://www.beerlab.org/ref.fa]], [[http://www.beerlab.org/alt.fa]] from [[http://www.beerlab.org/gkmsvm\|www.beerlab.org/gkmsvm]]

	1. generate GC, length, and repeat matched negative set and extract fasta sequence files for ctcfpos.fa and ctcfneg_1x.fa: (Larger negative sets can be generated by increasing xfold, and running time can be decreased by reducing nMaxTrials, at the cost of not matching difficult sequences. In general training on larger sequence sets will produce more accurate and robust models.)		1. generate GC, length, and repeat matched negative set and extract fasta sequence files for ctcfpos.fa and ctcfneg_1x.fa: (Larger negative sets can be generated by increasing xfold, and running time can be decreased by reducing nMaxTrials, at the cost of not matching difficult sequences. In general training on larger sequence sets will produce more accurate and robust models.)
Line 78:		Line 80:
	CCACTAGAGG 4.529869 <br/>		CCACTAGAGG 4.529869 <br/>
	CAGCAGAGGG 4.335304 <br/>		CAGCAGAGGG 4.335304 <br/>

			5. To calculate the impact of a variant, in this case on CTCF binding, we use gkmsvm_classify to find the
			score difference between two alleles given in FASTA format in ‘ref.fa’ and ‘alt.fa’. This is only different
			by a scale factor from deltaSVM calculated directly from SVM weights, as described in (Lee, Gorkin,
			Baker, Strober, Aasoni, McCallion, Beer, Nature Genetics 2015).

			> gkmsvm_delta('ref.fa','alt.fa',svmfnprfx='ctcf_1x', 'dsvm_ctcf_1x.out')


	If you find this tool useful, please cite:		If you find this tool useful, please cite:

>Admin at 18:56, 5 August 2019

2019-08-05T18:56:59Z

← Older revision		Revision as of 18:56, 5 August 2019
Line 76:		Line 76:
	CACTAGAGGG 4.610800 <br/>		CACTAGAGGG 4.610800 <br/>
	CACTAGGTGG 4.580834 <br/>		CACTAGGTGG 4.580834 <br/>
	CCACTAGAGG 4.529869 <br/>/		CCACTAGAGG 4.529869 <br/>
	CAGCAGAGGG 4.335304 <br/>		CAGCAGAGGG 4.335304 <br/>