FunSVPT - Revision history

Public: /* Building data context */

2014-04-08T01:41:30Z

Building data context

← Older revision		Revision as of 01:41, 8 April 2014
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	Please put files under directory ‘data/user_annotations’ or specific directory with option (-ua). The first field separated by ‘.’ will be used as annotation name. Please prepare your files in BED format and use the 4th column for additional information, if needed. We have placed repeat regions obtained from UCSC there as an example.		Please put files under directory ‘data/user_annotations’ or specific directory with option (-ua). The first field separated by ‘.’ will be used as annotation name. Please prepare your files in BED format and use the 4th column for additional information, if needed. We have placed repeat regions obtained from UCSC there as an example.

	* All of other files can be replaced with user-specific data. Please refer to the files under ‘data/’ to correctly format ~~the data~~.		* All of other files can be replaced with user-specific data. Please refer to the files under ‘data/’ to correctly format them.

Public: /* Building data context */

2014-04-08T01:38:54Z

Building data context

← Older revision		Revision as of 01:38, 8 April 2014
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	This is similar to ‘Add new networks’. Please put files under ‘data/cancer_recurrence’ and use the first field as the cancer type name. This file can be produced by running FunSVPT (file ‘Recur.Summary’ produced by the tool) on cancer samples of a particular type.		This is similar to ‘Add new networks’. Please put files under ‘data/cancer_recurrence’ and use the first field as the cancer type name. This file can be produced by running FunSVPT (file ‘Recur.Summary’ produced by the tool) on cancer samples of a particular type.

	* Add user-specific annotation sets, such as ~~epigenomics~~ modifications. Please put files under directory ‘data/user_annotations’ or ~~the specified~~ directory with option (-ua) ~~and use the~~ first field separated by ‘,’ as annotation name. Please prepare your files in BED format and use the 4th column for additional information, if needed. We have placed repeat regions obtained from UCSC there as an example ~~file~~.		* Add user-specific annotation sets, such as epigenetic modifications
			Please put files under directory ‘data/user_annotations’ or specific directory with option (-ua). The first field separated by ‘.’ will be used as annotation name. Please prepare your files in BED format and use the 4th column for additional information, if needed. We have placed repeat regions obtained from UCSC there as an example.

	* All of other files can be replaced with user-specific data. Please refer to the files under ‘data/’ to correctly format the data.		* All of other files can be replaced with user-specific data. Please refer to the files under ‘data/’ to correctly format the data.

Public: /* F. Output files */

2014-04-07T21:03:43Z

F. Output files

← Older revision		Revision as of 21:03, 7 April 2014
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	##INFO=<ID=CANG,Number=.,Type=String,Description="Prior Gene Information, e.g.[cancer][TF_regulating_known_cancer_gene]		##INFO=<ID=CANG,Number=.,Type=String,Description="Prior Gene Information, e.g.[cancer][TF_regulating_known_cancer_gene]
	[up_regulated][actionable]...";		[up_regulated][actionable]...";
	##INFO=<ID=CDSS,Number=.,Type=String,Description="~~FunSEQ~~ Coding Score">		##INFO=<ID=CDSS,Number=.,Type=String,Description="Coding Score">
	##INFO=<ID=NCDS,Number=.,Type=String,Description="~~FunSEQ~~ NonCoding Score">		##INFO=<ID=NCDS,Number=.,Type=String,Description="NonCoding Score">
	##INFO=<ID=RECUR,Number=.,Type=String,Description="Recurrent elements / variants">		##INFO=<ID=RECUR,Number=.,Type=String,Description="Recurrent elements / variants">
	##INFO=<ID=DBRECUR,Number=.,Type=String,Description="Recurrence database">		##INFO=<ID=DBRECUR,Number=.,Type=String,Description="Recurrence database">

Public: /* C. Pre-built Data Context */

2014-04-07T21:00:30Z

C. Pre-built Data Context

← Older revision		Revision as of 21:00, 7 April 2014
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	==C. Pre-built Data Context==		==C. Pre-built Data Context==
	All of the data can be downloaded under ‘Downloads’ in the web server. If you would like to use the data, please download and put them under ~~‘cmap~~-0.1/data’.		All of the data can be downloaded under ‘Downloads’ in the web server. If you would like to use the data, please download and put them under 'funsvpt-0.1/data’.

	==D. Tool Usage==		==D. Tool Usage==

Public: /* B. Tool installation */

2014-04-07T20:59:28Z

B. Tool installation

← Older revision		Revision as of 20:59, 7 April 2014
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	==B. Tool installation==		==B. Tool installation==
	This is a PERL- and Linux/UNIX-based tool. At the command-line prompt, type the following. The purpose is to write the path of ~~cmap~~.pm to your environment. <br>		This is a PERL- and Linux/UNIX-based tool. At the command-line prompt, type the following. The purpose is to write the path of funSVPT.pm to your environment. <br>

	$ tar xvf ~~cmap~~.v.0.1.tar		$ tar xvf funSVPT.v.0.1.tar
	$ cd ~~cmap~~-0.1/		$ cd funsvpt-0.1/
	$ cd ~~cmap~~/		$ cd funSVPT/
	$ perl Makefile.PL		$ perl Makefile.PL
	$ make		$ make
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	$ make install		$ make install
	If you don’t have the permission to modify the environment, open the ‘.bashrc’ file and add the following to the end of the file. Then ‘source .bashrc’. <br>		If you don’t have the permission to modify the environment, open the ‘.bashrc’ file and add the following to the end of the file. Then ‘source .bashrc’. <br>
	PERL5LIB=${PERL5LIB}: $path_of_the_tool/~~cmap~~-0.1/~~cmap~~/lib		PERL5LIB=${PERL5LIB}: $path_of_the_tool/funsvpt-0.1/funSVPT/lib
	export PERL5LIB		export PERL5LIB

Public: /* C. Pre-built Data Context */

2014-04-07T20:58:14Z

C. Pre-built Data Context

← Older revision		Revision as of 20:58, 7 April 2014
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	==C. Pre-built Data Context==		==C. Pre-built Data Context==
	All of the data can be downloaded under ‘Downloads’ in the web server. If you would like to use the data, please download and put them under ~~‘funsvpt~~-0.1/data’.		All of the data can be downloaded under ‘Downloads’ in the web server. If you would like to use the data, please download and put them under ‘cmap-0.1/data’.

	==D. Tool Usage==		==D. Tool Usage==

Public: /* B. Tool installation */

2014-04-07T20:57:46Z

B. Tool installation

← Older revision		Revision as of 20:57, 7 April 2014
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	==B. Tool installation==		==B. Tool installation==
	This is a PERL- and Linux/UNIX-based tool. At the command-line prompt, type the following. The purpose is to write the path of ~~funSVPT~~.pm to your environment. <br>		This is a PERL- and Linux/UNIX-based tool. At the command-line prompt, type the following. The purpose is to write the path of cmap.pm to your environment. <br>

	$ tar xvf ~~funSVPT~~.v.0.1.tar		$ tar xvf cmap.v.0.1.tar
	$ cd ~~funsvpt~~-0.1/		$ cd cmap-0.1/
	$ cd ~~funSVPT~~/		$ cd cmap/
	$ perl Makefile.PL		$ perl Makefile.PL
	$ make		$ make
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	$ make install		$ make install
	If you don’t have the permission to modify the environment, open the ‘.bashrc’ file and add the following to the end of the file. Then ‘source .bashrc’. <br>		If you don’t have the permission to modify the environment, open the ‘.bashrc’ file and add the following to the end of the file. Then ‘source .bashrc’. <br>
	PERL5LIB=${PERL5LIB}: $path_of_the_tool/~~funsvpt~~-0.1/~~funSVPT~~/lib		PERL5LIB=${PERL5LIB}: $path_of_the_tool/cmap-0.1/cmap/lib
	export PERL5LIB		export PERL5LIB

Public: /* A. Dependencies */

2014-04-07T20:56:48Z

A. Dependencies

← Older revision		Revision as of 20:56, 7 April 2014
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	* [http://sourceforge.net/projects/samtools/files/tabix/ tabix] (version tabix-0.2.6 and up) <br>		* [http://sourceforge.net/projects/samtools/files/tabix/ tabix] (version tabix-0.2.6 and up) <br>
	* [http://vat.gersteinlab.org/index.php VAT] (snpMapper, indelMapper Module) - A good installation guide for VAT can be found [http://ngsda.blogspot.com/2011/06/vat.html here]. <br>		* [http://vat.gersteinlab.org/index.php VAT] (snpMapper, indelMapper Module) - A good installation guide for VAT can be found [http://ngsda.blogspot.com/2011/06/vat.html here]. <br>
	<span style="font-size:88%; line-height: 1.3em;">If you are only interested in non-coding variants, you don't need to install VAT. But remember to use '-nc' option</span>		<span style="font-size:88%; line-height: 1.3em;">If you are only interested in non-coding variants, you don't need to install VAT. But remember to use '-nc' option.</span>
	<br>		<br>
	* [http://bioinfo.lifl.fr/TFM/TFMpvalue/ TFMpvalue-sc2pv] <br>		* [http://bioinfo.lifl.fr/TFM/TFMpvalue/ TFMpvalue-sc2pv] <br>

Public: /* A. Dependencies */

2014-04-07T20:56:28Z

A. Dependencies

← Older revision		Revision as of 20:56, 7 April 2014
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	* [http://sourceforge.net/projects/samtools/files/tabix/ tabix] (version tabix-0.2.6 and up) <br>		* [http://sourceforge.net/projects/samtools/files/tabix/ tabix] (version tabix-0.2.6 and up) <br>
	* [http://vat.gersteinlab.org/index.php VAT] (snpMapper, indelMapper Module) - A good installation guide for VAT can be found [http://ngsda.blogspot.com/2011/06/vat.html here]. <br>		* [http://vat.gersteinlab.org/index.php VAT] (snpMapper, indelMapper Module) - A good installation guide for VAT can be found [http://ngsda.blogspot.com/2011/06/vat.html here]. <br>
	<span style="font-size:88%; line-height: 1.3em;">If you are only interested in non-coding variants, you don't need to install VAT. But remember to use '-nc' option ~~in Funseq~~ </span>		<span style="font-size:88%; line-height: 1.3em;">If you are only interested in non-coding variants, you don't need to install VAT. But remember to use '-nc' option</span>
	<br>		<br>
	* [http://bioinfo.lifl.fr/TFM/TFMpvalue/ TFMpvalue-sc2pv] <br>		* [http://bioinfo.lifl.fr/TFM/TFMpvalue/ TFMpvalue-sc2pv] <br>

Public: /* E. Input files */

2014-04-02T21:45:34Z

E. Input files

← Older revision		Revision as of 21:45, 2 April 2014
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	End position - end coordinates of variants. (end exclusive)		End position - end coordinates of variants. (end exclusive)
	e.g., chr1 0 100 spanning bases numbered 0-99		e.g., chr1 0 100 spanning bases numbered 0-99
	Reference allele - ~~reference~~ allele of variants		Reference allele - germlime allele of variants
	Alternative allele - ~~alternative~~ allele of variants		Alternative allele - mutated allele of variants

	VCF format. The header line names the 8 fixed, mandatory columns. These columns are as follows (tab-delimited):		VCF format. The header line names the 8 fixed, mandatory columns. These columns are as follows (tab-delimited):