GersteinInfo - User contributions [en]

PeakSeq

2011-10-19T15:14:17Z

Arif.harmanci: /* Software download */

PeakSeq is a program for identifying and ranking peak regions in ChIP-Seq experiments. It takes as input, mapped reads from a ChIP-Seq experiment, mapped reads from a control experiment and outputs a file with peak regions ranked with increasing Q-values.

== Citation ==
PeakSeq algorithm is described in: Rozowsky J, Euskirchen G, Auerbach R, Zhang Z, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein M
Nature Biotechnology 27, 66 - 75 (2009).

== Software download ==
[http://archive.gersteinlab.org/proj/PeakSeq/Scoring_ChIPSeq/Code/C/PeakSeq.v1.1.tar.bz2 PeakSeq version 1.1]: Re-coded from scratch, runs slightly faster and it is easier to use, and supports multiple mapped read file formats. Refer to the README file in the archive for help on running PeakSeq. In addition, [http://archive.gersteinlab.org/proj/PeakSeq/peakseq_v.1.1.ppt these slides] may be helpful.

[http://archive.gersteinlab.org/proj/PeakSeq/Scoring_ChIPSeq/Code/C/PeakSeq_v1.01.tar.gz PeakSeq version 1.01]: Original PeakSeq code.

== Additional Resources Related to PeakSeq ==

Mapability maps for several organisms can be found [http://archive.gersteinlab.org/proj/PeakSeq/Mappability_Map/ here]

=== Datasets ===

Raw ChIP-Seq Sequence Data: [http://archive.gersteinlab.org/proj/PeakSeq/Sequence_Data/HeLa-S3 PolII], [http://archive.gersteinlab.org/proj/PeakSeq/Sequence_Data/Stimulated_HeLa-S3 STAT-1]

=== Yale Chip-seq Data Pipeline ===

[http://array.mbb.yale.edu/pipeline/illumina.html Illumina pipeline] (wrapper for Illumina pipeline)

[http://array.mbb.yale.edu/pipeline/scoring.html Chip-seq scoring pipeline] (runs PeakSeq)

Also, one might want to consider ChipSeqSim : http://papers.gersteinlab.org/papers/chip-seq-simu/

== Contact ==
Joel Rozowsky at joel DOT rozowsky AT yale DOT edu or Arif Harmanci at Arif DOT Harmanci AT yale DOT edu.

VAT/download

2011-06-14T15:30:10Z

Arif.harmanci: /* Installation */

<center>[http://archive.gersteinlab.org/proj/VAT '''VAT Main Page''']</center>

__TOC__

== External Software ==

<center>[[#top|Top]]</center>

=== Required ===

* [http://www.gnu.org/software/gsl/ GSL] - GNU Scientific Library (version-1.14; required for libBIOS, which is a general C library).
* [http://hgwdev.cse.ucsc.edu/~kent/exe/linux/blatSuite.34.zip BlatSuite] - BLAT and a collection of utility programs. These tools are utilized by VAT. Note: these executables must be part of the PATH.
* [http://www.libgd.org/Main_Page GD library] - The GD library is used to create an image for each gene model and its associated variants (version-2.0.35; required by VAT).
* [http://samtools.sourceforge.net/tabix.shtml Tabix] - Tabix (version-0.2.3) is a generic tool that indexes position-sorted files in tab-delimited formats to facilitate fast retrieval ([http://sourceforge.net/projects/samtools/files/tabix/ download]). These tools are utilized by VAT. Note: these executables must be part of the PATH.
* [http://rna.urmc.rochester.edu/RNAstructure.html RNAstructure] - RNAstructure is a software package for RNA structure prediction and analysis. This tool is utilized by VAT for prediction of structures for RNA sequences with and without the variants.
* [http://varna.lri.fr/downloads.html VARNA] - VARNA is a java applet for producing high quality RNA secondary structure plots. VAT utilizes VARNA for visualization of the RNA secondary structures.
 

<center>[[#top|Top]]</center>

=== Optional ===

* [http://vcftools.sourceforge.net/index.html VCF tools] - VCF tools consists of a suite of useful modules to manipulate VCF files.

 

== VAT Download ==

 

<pre>
Important Note
==============

THIS PACKAGE (VAT) IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESSED OR IMPLIED
WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES
OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
</pre>

 

<center>[[#top|Top]]</center>

=== Source code ===

VAT is a based on a general C library, called libBIOS. A TAR ball of libBIOS and VAT can be downloaded here:
* [http://archive.gersteinlab.org/proj/VAT/src libBIOS-1.1.0.tar.gz]
* [http://archive.gersteinlab.org/proj/VAT/src VAT-0.5.tar.gz] - Initial upload

 

<center>[[#top|Top]]</center>

=== Executables ===

Statically built binaries for UNIX can be found here:
* [http://archive.gersteinlab.org/proj/VAT/src VAT-0.5-UNIX.tar.gz] - 64bit version

 

<center>[[#top|Top]]</center>

=== License information ===

The software package is released under the [http://creativecommons.org/licenses/by-nc/2.5/legalcode Creative Commons license (Attribution-NonCommerical)]. 
For more details please refer to the [http://www.gersteinlab.org/misc/permissions.html Permissions Page] on the Gerstein Lab webpage.

 

== Installation ==

<center>[[#top|Top]]</center>

=== Installation of the external GSL and GD libraries ===

In order to install VAT two external libraries must be installed first. The libBIOS library depends on GSL, whereas VAT makes use of the GD library. Please follow the instructions provided by each package. The GSL library can be installed on most systems using the following commands (for details, please refer to the specific instructions at the [http://www.gnu.org/software/gsl/ GNU Scientific Library] website):
<pre>
$ cd /path/to/gsl-1.14/
$ ./configure --prefix=`pwd`
$ make
$ make install
</pre>

Similarly, the [http://www.libgd.org/Main_Page GD library] can be installed on most systems with the following commands:
<pre>
$ cd /path/to/gd-2.0.35/
$ ./configure --prefix=`pwd` --with-jpeg=/path/to/jpegLib/
$ make
$ make install
</pre>

After they are installed, the first step to install VAT is the installation and configuration of libBIOS.

 

<center>[[#top|Top]]</center>

=== Installation and Configuration of libBIOS ===

Depending on where the three libraries (GSL, libBIOS, and GD) are installed, the following variables need to be set:

<pre>
export CPPFLAGS="-I/path/to/gsl-1.14/include -I/path/to/libbios/include -I/path/to/gd-2.0.35/include"
export LDFLAGS="-L/path/to/gsl-1.14/lib -L/path/to/libbios/lib -L/path/to/gd-2.0.35/lib"
</pre>

libBIOS can be installed on most systems with the following commands:
<pre>
$ cd /path/to/libbios-x.x.x/
$ ./configure --prefix=`pwd`
$ make
$ make install
</pre>

 

=== Installation of RNAstructure and VARNA ===
Download RNAstructure and follow the building instructions. Make sure that the build directory is included in PATH enrivonment variable. In addition, RNAstructure needs an environment variable named DATAPATH to be set to the directory of thermodynamic parameter files that are distributed with RNAstructure package.

Download VARNA jar file and add the jar file path to CLASSPATH enrivonment variable.

<center>[[#top|Top]]</center>

=== Installation and Configuration of VAT ===

A few simple steps are required to install VAT:
<pre>
$ cd /path/to/vat-x.x.x/
$ ./configure --prefix=`pwd`
$ make
$ make install
</pre>

VAT contains a configuration file ('''vatConfirgurationTemplate.txt'''), which contains a set of variables that are used by a number of different programs. The name/value pairs are space or tab-delimited. Empty lines are lines starting with '//' are ignored.
<pre>

// ===============================================================================
// REQUIRED
// ===============================================================================

// Tabix directory (includes both tabix and bgzip)
TABIX_DIR /path/to/tabix-0.2.3

// ===============================================================================
// OPTIONAL (required only for CGIs)
// ===============================================================================

// CGI base URL (where the CGIs are located)
WEB_URL_CGI http://webserver.org/path

// Path to the web data directory where the preprocessed files are stored
WEB_DATA_DIR /path/to/public_html/path/to/VAT
// URL to preprocessed files
WEB_DATA_URL http://webserver.org/path/to/VAT

</pre>

This file has to be '''configured properly''' by filling in the required information. Subsequently, the following environment variable ('''VAT_CONFIG_FILE''') has to be set:

VAT_CONFIG_FILE=/pathTo/vat/vatConfirgurationTemplate.txt

 

== Setup of the web server ==

 

This step is optional, but useful for visualizing the results of processed data sets. The following steps are required:

* The executable '''vat_cgi''' has to be located in the cgi-bin directory on the web server
* The configuration file ('''vatConfirgurationTemplate.txt''') must contain the pertinent information
* The following .htaccess file should be added to the cgi-bin:
SetEnv VAT_CONFIG_FILE /path/to/vatConfirgurationTemplate.txt
* The web data directory (defined by WEB_DATA_DIR in the configuration file) requires the following information:
** '''Preprocessed annotation sets''' (gencode3b.interval, gencode3b.fa, gencode3c.interval, gencode3c.fa)
** The '''tabix''' and '''bgzip''' executables
** Two images provided by the VAT source code: '''check.png''' and '''processing.gif''' (referred to by vat_cgi)
** Directory that has the same name as the data set (in this example: SampleData). This directory contains the images for each gene (created by [http://info.gersteinlab.org/VAT#vcf2images vcf2images]) and a VCF file for each gene (created by [http://info.gersteinlab.org/VAT#vcfSubsetByGene vcfSubsetByGene])
*** SampleData
*** SampleData.vcf.gz
*** SampleData.vcf.gz.tbi
*** SampleData.sampleSummary.txt (generated by [http://info.gersteinlab.org/VAT#vcfSummary vcfSummary])
*** SampleData.geneSummary.txt (generated by [http://info.gersteinlab.org/VAT#vcfSummary vcfSummary])

For additional information please refer to the [http://info.gersteinlab.org/VAT#Setting_up_the_web_server example workflow].

 

== Download of pre-processed annotation sets ==

 

The following annotation sets are derived from the [http://www.gencodegenes.org/ GENCODE] project. Each each entry has a set of '''transcript coordinates''' (in [http://info.gersteinlab.org/VAT#Interval Interval] format) and a set of '''transcript sequences''' (introns removed; sequence with respect to the '+' strand; in FASTA format)

* Coding sequence (CDS) elements where the both the ''gene_type'' and ''transcript_type'' are ''protein_coding'':
** GENCODE version 3b (hg18): [http://homes.gersteinlab.org/people/lh372/VAT/gencode3b.interval Transcript coordinates], [http://homes.gersteinlab.org/people/lh372/VAT/gencode3b.fa Transcript sequences]
** GENCODE version 3c (hg19): [http://homes.gersteinlab.org/people/lh372/VAT/gencode3c.interval Transcript coordinates], [http://homes.gersteinlab.org/people/lh372/VAT/gencode3c.fa Transcript sequences]
** GENCODE version 4 (hg19): [http://homes.gersteinlab.org/people/lh372/VAT/gencode4.interval Transcript coordinates], [http://homes.gersteinlab.org/people/lh372/VAT/gencode4.fa Transcript sequences]
** GENCODE version 5 (hg19): [http://homes.gersteinlab.org/people/lh372/VAT/gencode5.interval Transcript coordinates], [http://homes.gersteinlab.org/people/lh372/VAT/gencode5.fa Transcript sequences]
** GENCODE version 6 (hg19): [http://homes.gersteinlab.org/people/lh372/VAT/gencode6.interval Transcript coordinates], [http://homes.gersteinlab.org/people/lh372/VAT/gencode6.fa Transcript sequences]
** GENCODE version 7 (hg19): [http://homes.gersteinlab.org/people/lh372/VAT/gencode7.interval Transcript coordinates], [http://homes.gersteinlab.org/people/lh372/VAT/gencode7.fa Transcript sequences]

 

* miRNAs where ''gene_type'' is ''miRNA'':
** GENCODE version 3b (hg18): [http://homes.gersteinlab.org/people/lh372/VAT/gencode3b.miRNA.interval Transcript coordinates], [http://homes.gersteinlab.org/people/lh372/VAT/gencode3b.miRNA.fa Transcript sequences]
** GENCODE version 3c (hg19): [http://homes.gersteinlab.org/people/lh372/VAT/gencode3c.miRNA.interval Transcript coordinates], [http://homes.gersteinlab.org/people/lh372/VAT/gencode3c.miRNA.fa Transcript sequences]
** GENCODE version 4 (hg19): [http://homes.gersteinlab.org/people/lh372/VAT/gencode4.miRNA.interval Transcript coordinates], [http://homes.gersteinlab.org/people/lh372/VAT/gencode4.miRNA.fa Transcript sequences]
** GENCODE version 5 (hg19): [http://homes.gersteinlab.org/people/lh372/VAT/gencode5.miRNA.interval Transcript coordinates], [http://homes.gersteinlab.org/people/lh372/VAT/gencode5.miRNA.fa Transcript sequences]
** GENCODE version 6 (hg19): [http://homes.gersteinlab.org/people/lh372/VAT/gencode6.miRNA.interval Transcript coordinates], [http://homes.gersteinlab.org/people/lh372/VAT/gencode6.miRNA.fa Transcript sequences]
** GENCODE version 7 (hg19): [http://homes.gersteinlab.org/people/lh372/VAT/gencode7.miRNA.interval Transcript coordinates], [http://homes.gersteinlab.org/people/lh372/VAT/gencode7.miRNA.fa Transcript sequences]

VAT/download

2011-06-14T15:19:21Z

Arif.harmanci: /* Required */

<center>[http://archive.gersteinlab.org/proj/VAT '''VAT Main Page''']</center>

__TOC__

== External Software ==

<center>[[#top|Top]]</center>

=== Required ===

* [http://www.gnu.org/software/gsl/ GSL] - GNU Scientific Library (version-1.14; required for libBIOS, which is a general C library).
* [http://hgwdev.cse.ucsc.edu/~kent/exe/linux/blatSuite.34.zip BlatSuite] - BLAT and a collection of utility programs. These tools are utilized by VAT. Note: these executables must be part of the PATH.
* [http://www.libgd.org/Main_Page GD library] - The GD library is used to create an image for each gene model and its associated variants (version-2.0.35; required by VAT).
* [http://samtools.sourceforge.net/tabix.shtml Tabix] - Tabix (version-0.2.3) is a generic tool that indexes position-sorted files in tab-delimited formats to facilitate fast retrieval ([http://sourceforge.net/projects/samtools/files/tabix/ download]). These tools are utilized by VAT. Note: these executables must be part of the PATH.
* [http://rna.urmc.rochester.edu/RNAstructure.html RNAstructure] - RNAstructure is a software package for RNA structure prediction and analysis. This tool is utilized by VAT for prediction of structures for RNA sequences with and without the variants.
* [http://varna.lri.fr/downloads.html VARNA] - VARNA is a java applet for producing high quality RNA secondary structure plots. VAT utilizes VARNA for visualization of the RNA secondary structures.
 

<center>[[#top|Top]]</center>

=== Optional ===

* [http://vcftools.sourceforge.net/index.html VCF tools] - VCF tools consists of a suite of useful modules to manipulate VCF files.

 

== VAT Download ==

 

<pre>
Important Note
==============

THIS PACKAGE (VAT) IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESSED OR IMPLIED
WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES
OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
</pre>

 

<center>[[#top|Top]]</center>

=== Source code ===

VAT is a based on a general C library, called libBIOS. A TAR ball of libBIOS and VAT can be downloaded here:
* [http://archive.gersteinlab.org/proj/VAT/src libBIOS-1.1.0.tar.gz]
* [http://archive.gersteinlab.org/proj/VAT/src VAT-0.5.tar.gz] - Initial upload

 

<center>[[#top|Top]]</center>

=== Executables ===

Statically built binaries for UNIX can be found here:
* [http://archive.gersteinlab.org/proj/VAT/src VAT-0.5-UNIX.tar.gz] - 64bit version

 

<center>[[#top|Top]]</center>

=== License information ===

The software package is released under the [http://creativecommons.org/licenses/by-nc/2.5/legalcode Creative Commons license (Attribution-NonCommerical)]. 
For more details please refer to the [http://www.gersteinlab.org/misc/permissions.html Permissions Page] on the Gerstein Lab webpage.

 

== Installation ==

<center>[[#top|Top]]</center>

=== Installation of the external GSL and GD libraries ===

In order to install VAT two external libraries must be installed first. The libBIOS library depends on GSL, whereas VAT makes use of the GD library. Please follow the instructions provided by each package. The GSL library can be installed on most systems using the following commands (for details, please refer to the specific instructions at the [http://www.gnu.org/software/gsl/ GNU Scientific Library] website):
<pre>
$ cd /path/to/gsl-1.14/
$ ./configure --prefix=`pwd`
$ make
$ make install
</pre>

Similarly, the [http://www.libgd.org/Main_Page GD library] can be installed on most systems with the following commands:
<pre>
$ cd /path/to/gd-2.0.35/
$ ./configure --prefix=`pwd` --with-jpeg=/path/to/jpegLib/
$ make
$ make install
</pre>

After they are installed, the first step to install VAT is the installation and configuration of libBIOS.

 

<center>[[#top|Top]]</center>

=== Installation and Configuration of libBIOS ===

Depending on where the three libraries (GSL, libBIOS, and GD) are installed, the following variables need to be set:

<pre>
export CPPFLAGS="-I/path/to/gsl-1.14/include -I/path/to/libbios/include -I/path/to/gd-2.0.35/include"
export LDFLAGS="-L/path/to/gsl-1.14/lib -L/path/to/libbios/lib -L/path/to/gd-2.0.35/lib"
</pre>

libBIOS can be installed on most systems with the following commands:
<pre>
$ cd /path/to/libbios-x.x.x/
$ ./configure --prefix=`pwd`
$ make
$ make install
</pre>

 

<center>[[#top|Top]]</center>

=== Installation and Configuration of VAT ===

A few simple steps are required to install VAT:
<pre>
$ cd /path/to/vat-x.x.x/
$ ./configure --prefix=`pwd`
$ make
$ make install
</pre>

VAT contains a configuration file ('''vatConfirgurationTemplate.txt'''), which contains a set of variables that are used by a number of different programs. The name/value pairs are space or tab-delimited. Empty lines are lines starting with '//' are ignored.
<pre>

// ===============================================================================
// REQUIRED
// ===============================================================================

// Tabix directory (includes both tabix and bgzip)
TABIX_DIR /path/to/tabix-0.2.3

// ===============================================================================
// OPTIONAL (required only for CGIs)
// ===============================================================================

// CGI base URL (where the CGIs are located)
WEB_URL_CGI http://webserver.org/path

// Path to the web data directory where the preprocessed files are stored
WEB_DATA_DIR /path/to/public_html/path/to/VAT
// URL to preprocessed files
WEB_DATA_URL http://webserver.org/path/to/VAT

</pre>

This file has to be '''configured properly''' by filling in the required information. Subsequently, the following environment variable ('''VAT_CONFIG_FILE''') has to be set:

VAT_CONFIG_FILE=/pathTo/vat/vatConfirgurationTemplate.txt

 

== Setup of the web server ==

 

This step is optional, but useful for visualizing the results of processed data sets. The following steps are required:

* The executable '''vat_cgi''' has to be located in the cgi-bin directory on the web server
* The configuration file ('''vatConfirgurationTemplate.txt''') must contain the pertinent information
* The following .htaccess file should be added to the cgi-bin:
SetEnv VAT_CONFIG_FILE /path/to/vatConfirgurationTemplate.txt
* The web data directory (defined by WEB_DATA_DIR in the configuration file) requires the following information:
** '''Preprocessed annotation sets''' (gencode3b.interval, gencode3b.fa, gencode3c.interval, gencode3c.fa)
** The '''tabix''' and '''bgzip''' executables
** Two images provided by the VAT source code: '''check.png''' and '''processing.gif''' (referred to by vat_cgi)
** Directory that has the same name as the data set (in this example: SampleData). This directory contains the images for each gene (created by [http://info.gersteinlab.org/VAT#vcf2images vcf2images]) and a VCF file for each gene (created by [http://info.gersteinlab.org/VAT#vcfSubsetByGene vcfSubsetByGene])
*** SampleData
*** SampleData.vcf.gz
*** SampleData.vcf.gz.tbi
*** SampleData.sampleSummary.txt (generated by [http://info.gersteinlab.org/VAT#vcfSummary vcfSummary])
*** SampleData.geneSummary.txt (generated by [http://info.gersteinlab.org/VAT#vcfSummary vcfSummary])

For additional information please refer to the [http://info.gersteinlab.org/VAT#Setting_up_the_web_server example workflow].

 

== Download of pre-processed annotation sets ==

 

The following annotation sets are derived from the [http://www.gencodegenes.org/ GENCODE] project. Each each entry has a set of '''transcript coordinates''' (in [http://info.gersteinlab.org/VAT#Interval Interval] format) and a set of '''transcript sequences''' (introns removed; sequence with respect to the '+' strand; in FASTA format)

* Coding sequence (CDS) elements where the both the ''gene_type'' and ''transcript_type'' are ''protein_coding'':
** GENCODE version 3b (hg18): [http://homes.gersteinlab.org/people/lh372/VAT/gencode3b.interval Transcript coordinates], [http://homes.gersteinlab.org/people/lh372/VAT/gencode3b.fa Transcript sequences]
** GENCODE version 3c (hg19): [http://homes.gersteinlab.org/people/lh372/VAT/gencode3c.interval Transcript coordinates], [http://homes.gersteinlab.org/people/lh372/VAT/gencode3c.fa Transcript sequences]
** GENCODE version 4 (hg19): [http://homes.gersteinlab.org/people/lh372/VAT/gencode4.interval Transcript coordinates], [http://homes.gersteinlab.org/people/lh372/VAT/gencode4.fa Transcript sequences]
** GENCODE version 5 (hg19): [http://homes.gersteinlab.org/people/lh372/VAT/gencode5.interval Transcript coordinates], [http://homes.gersteinlab.org/people/lh372/VAT/gencode5.fa Transcript sequences]
** GENCODE version 6 (hg19): [http://homes.gersteinlab.org/people/lh372/VAT/gencode6.interval Transcript coordinates], [http://homes.gersteinlab.org/people/lh372/VAT/gencode6.fa Transcript sequences]
** GENCODE version 7 (hg19): [http://homes.gersteinlab.org/people/lh372/VAT/gencode7.interval Transcript coordinates], [http://homes.gersteinlab.org/people/lh372/VAT/gencode7.fa Transcript sequences]

 

* miRNAs where ''gene_type'' is ''miRNA'':
** GENCODE version 3b (hg18): [http://homes.gersteinlab.org/people/lh372/VAT/gencode3b.miRNA.interval Transcript coordinates], [http://homes.gersteinlab.org/people/lh372/VAT/gencode3b.miRNA.fa Transcript sequences]
** GENCODE version 3c (hg19): [http://homes.gersteinlab.org/people/lh372/VAT/gencode3c.miRNA.interval Transcript coordinates], [http://homes.gersteinlab.org/people/lh372/VAT/gencode3c.miRNA.fa Transcript sequences]
** GENCODE version 4 (hg19): [http://homes.gersteinlab.org/people/lh372/VAT/gencode4.miRNA.interval Transcript coordinates], [http://homes.gersteinlab.org/people/lh372/VAT/gencode4.miRNA.fa Transcript sequences]
** GENCODE version 5 (hg19): [http://homes.gersteinlab.org/people/lh372/VAT/gencode5.miRNA.interval Transcript coordinates], [http://homes.gersteinlab.org/people/lh372/VAT/gencode5.miRNA.fa Transcript sequences]
** GENCODE version 6 (hg19): [http://homes.gersteinlab.org/people/lh372/VAT/gencode6.miRNA.interval Transcript coordinates], [http://homes.gersteinlab.org/people/lh372/VAT/gencode6.miRNA.fa Transcript sequences]
** GENCODE version 7 (hg19): [http://homes.gersteinlab.org/people/lh372/VAT/gencode7.miRNA.interval Transcript coordinates], [http://homes.gersteinlab.org/people/lh372/VAT/gencode7.miRNA.fa Transcript sequences]

VAT/download

2011-06-14T15:18:26Z

Arif.harmanci: /* Required */

<center>[http://archive.gersteinlab.org/proj/VAT '''VAT Main Page''']</center>

__TOC__

== External Software ==

<center>[[#top|Top]]</center>

=== Required ===

* [http://www.gnu.org/software/gsl/ GSL] - GNU Scientific Library (version-1.14; required for libBIOS, which is a general C library).
* [http://hgwdev.cse.ucsc.edu/~kent/exe/linux/blatSuite.34.zip BlatSuite] - BLAT and a collection of utility programs. These tools are utilized by VAT. Note: these executables must be part of the PATH.
* [http://www.libgd.org/Main_Page GD library] - The GD library is used to create an image for each gene model and its associated variants (version-2.0.35; required by VAT).
* [http://samtools.sourceforge.net/tabix.shtml Tabix] - Tabix (version-0.2.3) is a generic tool that indexes position-sorted files in tab-delimited formats to facilitate fast retrieval ([http://sourceforge.net/projects/samtools/files/tabix/ download]). These tools are utilized by VAT. Note: these executables must be part of the PATH.
* [http://rna.urmc.rochester.edu/RNAstructure.html] - RNAstructure is a software package for RNA structure prediction and analysis. This tools is utilized by VAT for prediction of structures for RNA sequences with and without the variants.
* [http://varna.lri.fr/downloads.html] - VARNA is a java applet for producing high quality RNA secondary structure plots. VAT utilizes VARNA for visualization of the RNA secondary structures.
 

<center>[[#top|Top]]</center>

=== Optional ===

* [http://vcftools.sourceforge.net/index.html VCF tools] - VCF tools consists of a suite of useful modules to manipulate VCF files.

 

== VAT Download ==

 

<pre>
Important Note
==============

THIS PACKAGE (VAT) IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESSED OR IMPLIED
WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES
OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
</pre>

 

<center>[[#top|Top]]</center>

=== Source code ===

VAT is a based on a general C library, called libBIOS. A TAR ball of libBIOS and VAT can be downloaded here:
* [http://archive.gersteinlab.org/proj/VAT/src libBIOS-1.1.0.tar.gz]
* [http://archive.gersteinlab.org/proj/VAT/src VAT-0.5.tar.gz] - Initial upload

 

<center>[[#top|Top]]</center>

=== Executables ===

Statically built binaries for UNIX can be found here:
* [http://archive.gersteinlab.org/proj/VAT/src VAT-0.5-UNIX.tar.gz] - 64bit version

 

<center>[[#top|Top]]</center>

=== License information ===

The software package is released under the [http://creativecommons.org/licenses/by-nc/2.5/legalcode Creative Commons license (Attribution-NonCommerical)]. 
For more details please refer to the [http://www.gersteinlab.org/misc/permissions.html Permissions Page] on the Gerstein Lab webpage.

 

== Installation ==

<center>[[#top|Top]]</center>

=== Installation of the external GSL and GD libraries ===

In order to install VAT two external libraries must be installed first. The libBIOS library depends on GSL, whereas VAT makes use of the GD library. Please follow the instructions provided by each package. The GSL library can be installed on most systems using the following commands (for details, please refer to the specific instructions at the [http://www.gnu.org/software/gsl/ GNU Scientific Library] website):
<pre>
$ cd /path/to/gsl-1.14/
$ ./configure --prefix=`pwd`
$ make
$ make install
</pre>

Similarly, the [http://www.libgd.org/Main_Page GD library] can be installed on most systems with the following commands:
<pre>
$ cd /path/to/gd-2.0.35/
$ ./configure --prefix=`pwd` --with-jpeg=/path/to/jpegLib/
$ make
$ make install
</pre>

After they are installed, the first step to install VAT is the installation and configuration of libBIOS.

 

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=== Installation and Configuration of libBIOS ===

Depending on where the three libraries (GSL, libBIOS, and GD) are installed, the following variables need to be set:

<pre>
export CPPFLAGS="-I/path/to/gsl-1.14/include -I/path/to/libbios/include -I/path/to/gd-2.0.35/include"
export LDFLAGS="-L/path/to/gsl-1.14/lib -L/path/to/libbios/lib -L/path/to/gd-2.0.35/lib"
</pre>

libBIOS can be installed on most systems with the following commands:
<pre>
$ cd /path/to/libbios-x.x.x/
$ ./configure --prefix=`pwd`
$ make
$ make install
</pre>

 

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=== Installation and Configuration of VAT ===

A few simple steps are required to install VAT:
<pre>
$ cd /path/to/vat-x.x.x/
$ ./configure --prefix=`pwd`
$ make
$ make install
</pre>

VAT contains a configuration file ('''vatConfirgurationTemplate.txt'''), which contains a set of variables that are used by a number of different programs. The name/value pairs are space or tab-delimited. Empty lines are lines starting with '//' are ignored.
<pre>

// ===============================================================================
// REQUIRED
// ===============================================================================

// Tabix directory (includes both tabix and bgzip)
TABIX_DIR /path/to/tabix-0.2.3

// ===============================================================================
// OPTIONAL (required only for CGIs)
// ===============================================================================

// CGI base URL (where the CGIs are located)
WEB_URL_CGI http://webserver.org/path

// Path to the web data directory where the preprocessed files are stored
WEB_DATA_DIR /path/to/public_html/path/to/VAT
// URL to preprocessed files
WEB_DATA_URL http://webserver.org/path/to/VAT

</pre>

This file has to be '''configured properly''' by filling in the required information. Subsequently, the following environment variable ('''VAT_CONFIG_FILE''') has to be set:

VAT_CONFIG_FILE=/pathTo/vat/vatConfirgurationTemplate.txt

 

== Setup of the web server ==

 

This step is optional, but useful for visualizing the results of processed data sets. The following steps are required:

* The executable '''vat_cgi''' has to be located in the cgi-bin directory on the web server
* The configuration file ('''vatConfirgurationTemplate.txt''') must contain the pertinent information
* The following .htaccess file should be added to the cgi-bin:
SetEnv VAT_CONFIG_FILE /path/to/vatConfirgurationTemplate.txt
* The web data directory (defined by WEB_DATA_DIR in the configuration file) requires the following information:
** '''Preprocessed annotation sets''' (gencode3b.interval, gencode3b.fa, gencode3c.interval, gencode3c.fa)
** The '''tabix''' and '''bgzip''' executables
** Two images provided by the VAT source code: '''check.png''' and '''processing.gif''' (referred to by vat_cgi)
** Directory that has the same name as the data set (in this example: SampleData). This directory contains the images for each gene (created by [http://info.gersteinlab.org/VAT#vcf2images vcf2images]) and a VCF file for each gene (created by [http://info.gersteinlab.org/VAT#vcfSubsetByGene vcfSubsetByGene])
*** SampleData
*** SampleData.vcf.gz
*** SampleData.vcf.gz.tbi
*** SampleData.sampleSummary.txt (generated by [http://info.gersteinlab.org/VAT#vcfSummary vcfSummary])
*** SampleData.geneSummary.txt (generated by [http://info.gersteinlab.org/VAT#vcfSummary vcfSummary])

For additional information please refer to the [http://info.gersteinlab.org/VAT#Setting_up_the_web_server example workflow].

 

== Download of pre-processed annotation sets ==

 

The following annotation sets are derived from the [http://www.gencodegenes.org/ GENCODE] project. Each each entry has a set of '''transcript coordinates''' (in [http://info.gersteinlab.org/VAT#Interval Interval] format) and a set of '''transcript sequences''' (introns removed; sequence with respect to the '+' strand; in FASTA format)

* Coding sequence (CDS) elements where the both the ''gene_type'' and ''transcript_type'' are ''protein_coding'':
** GENCODE version 3b (hg18): [http://homes.gersteinlab.org/people/lh372/VAT/gencode3b.interval Transcript coordinates], [http://homes.gersteinlab.org/people/lh372/VAT/gencode3b.fa Transcript sequences]
** GENCODE version 3c (hg19): [http://homes.gersteinlab.org/people/lh372/VAT/gencode3c.interval Transcript coordinates], [http://homes.gersteinlab.org/people/lh372/VAT/gencode3c.fa Transcript sequences]
** GENCODE version 4 (hg19): [http://homes.gersteinlab.org/people/lh372/VAT/gencode4.interval Transcript coordinates], [http://homes.gersteinlab.org/people/lh372/VAT/gencode4.fa Transcript sequences]
** GENCODE version 5 (hg19): [http://homes.gersteinlab.org/people/lh372/VAT/gencode5.interval Transcript coordinates], [http://homes.gersteinlab.org/people/lh372/VAT/gencode5.fa Transcript sequences]
** GENCODE version 6 (hg19): [http://homes.gersteinlab.org/people/lh372/VAT/gencode6.interval Transcript coordinates], [http://homes.gersteinlab.org/people/lh372/VAT/gencode6.fa Transcript sequences]
** GENCODE version 7 (hg19): [http://homes.gersteinlab.org/people/lh372/VAT/gencode7.interval Transcript coordinates], [http://homes.gersteinlab.org/people/lh372/VAT/gencode7.fa Transcript sequences]

 

* miRNAs where ''gene_type'' is ''miRNA'':
** GENCODE version 3b (hg18): [http://homes.gersteinlab.org/people/lh372/VAT/gencode3b.miRNA.interval Transcript coordinates], [http://homes.gersteinlab.org/people/lh372/VAT/gencode3b.miRNA.fa Transcript sequences]
** GENCODE version 3c (hg19): [http://homes.gersteinlab.org/people/lh372/VAT/gencode3c.miRNA.interval Transcript coordinates], [http://homes.gersteinlab.org/people/lh372/VAT/gencode3c.miRNA.fa Transcript sequences]
** GENCODE version 4 (hg19): [http://homes.gersteinlab.org/people/lh372/VAT/gencode4.miRNA.interval Transcript coordinates], [http://homes.gersteinlab.org/people/lh372/VAT/gencode4.miRNA.fa Transcript sequences]
** GENCODE version 5 (hg19): [http://homes.gersteinlab.org/people/lh372/VAT/gencode5.miRNA.interval Transcript coordinates], [http://homes.gersteinlab.org/people/lh372/VAT/gencode5.miRNA.fa Transcript sequences]
** GENCODE version 6 (hg19): [http://homes.gersteinlab.org/people/lh372/VAT/gencode6.miRNA.interval Transcript coordinates], [http://homes.gersteinlab.org/people/lh372/VAT/gencode6.miRNA.fa Transcript sequences]
** GENCODE version 7 (hg19): [http://homes.gersteinlab.org/people/lh372/VAT/gencode7.miRNA.interval Transcript coordinates], [http://homes.gersteinlab.org/people/lh372/VAT/gencode7.miRNA.fa Transcript sequences]