FusionSeq Requirements - Revision history

Asboner: /* Human genome GRCh37/hg19 */

2011-05-07T11:53:39Z

Human genome GRCh37/hg19

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	=====Human genome GRCh37/hg19=====		=====Human genome GRCh37/hg19=====
	The corresponding version of these files for hg19 can be found [http://rnaseq.gersteinlab.org/fusionseq/tarballs/FusionSeq_Annotation_Data_hg19_1.0.tar.gz here (hg19)]~~. Please note that this data set has not been thoroughly tested yet. This means that it should work anyway~~.		The corresponding version of these files for hg19 can be found [http://rnaseq.gersteinlab.org/fusionseq/tarballs/FusionSeq_Annotation_Data_hg19_1.0.tar.gz here (hg19)].

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

Asboner: /* Provided */

2011-05-07T11:53:23Z

Provided

← Older revision		Revision as of 11:53, 7 May 2011
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	<pre>		<pre>
	$ bowtie-build -f knownGeneAnnotationTranscriptCompositeModel.fa		$ bowtie-build -f knownGeneAnnotationTranscriptCompositeModel.fa
	/~~path2bowtieIndex~~/hg18_knownGeneAnnotationTranscriptCompositeModel/hg18_knownGeneAnnotationTranscriptCompositeModel		/path/to/bowtie/Index/hg18_knownGeneAnnotationTranscriptCompositeModel/hg18_knownGeneAnnotationTranscriptCompositeModel
	</pre>		</pre>
	knownGeneAnnotationTranscriptCompositeModel.txt (the interval file) and knownGeneAnnotationTranscriptCompositeModel.fa (the sequences) should be located in the same directory.		knownGeneAnnotationTranscriptCompositeModel.txt (the interval file) and knownGeneAnnotationTranscriptCompositeModel.fa (the sequences) should be located in the same directory.

Asboner: /* External */

2011-05-07T11:53:00Z

External

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	*[http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/ Homo Sapiens Reference genome (hg18)]: the user should download both chromFa.zip and hg18.2bit.		*[http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/ Homo Sapiens Reference genome (hg18)]: the user should download both chromFa.zip and hg18.2bit.
	The human genome needs to be properly indexed to be used by bowtie. Please see the instruction of bowtie for performing this operation. Indicatevely, you would need to run something like:		The human genome needs to be properly indexed to be used by bowtie. Please see the instruction of bowtie for performing this operation. Indicatevely, you would need to run something like:
	$ bowtie-build -f hg18_nh.fa /~~path2bowtieIndex~~/hg18_nh/hg18_nh		$ bowtie-build -f hg18_nh.fa /path/to/bowtie/Index/hg18_nh/hg18_nh
	where '''hg18_nh.fa''' corresponds to the concatenation of all human chromosomes from chromFa.zip ''without'' the different haplotypes and the "random" sequences.		where '''hg18_nh.fa''' corresponds to the concatenation of all human chromosomes from chromFa.zip ''without'' the different haplotypes and the "random" sequences.

Asboner: /* Drawing tools */

2011-05-07T11:52:09Z

Drawing tools

← Older revision		Revision as of 11:52, 7 May 2011
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	===Drawing tools===		===Drawing tools===
	* [http://www.boutell.com/gd/ GD library]: The gd library is used to create schematic images of the PE reads connecting the two genes. It is required by [[FusionSeq_List_of_programs#gfr2images\|gfr2images]], which is an optional component of FusionSeq.		* [http://www.boutell.com/gd/ GD library]: The gd library is used to create schematic images of the PE reads connecting the two genes. It is required by [[FusionSeq_List_of_programs#gfr2images\|gfr2images]], which is an optional component of FusionSeq. As a reference, we tested FusionSeq with gd-2.0.35.

	===Data analysis===		===Data analysis===

Asboner: /* Scientific and bioinformatics libraries */

2011-05-07T11:51:38Z

Scientific and bioinformatics libraries

← Older revision		Revision as of 11:51, 7 May 2011
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	===Scientific and bioinformatics libraries===		===Scientific and bioinformatics libraries===
	* [http://www.gnu.org/software/gsl/ GNU Scientific Library (GSL)]: this library is a required for the compilation of [http://rnaseq.gersteinlab.org/doc/bios/ BIOS].		* [http://www.gnu.org/software/gsl/ GNU Scientific Library (GSL)]: this library is a required for the compilation of [http://rnaseq.gersteinlab.org/doc/bios/ BIOS]. As a reference, we tested FusionSeq with gsl-1.14.
	=====(versions 0.7.0 and later)=====		=====(versions 0.7.0 and later)=====
	* Starting with version 0.7.0, two new libraries are required:		* Starting with version 0.7.0, two new libraries are required:

Asboner: /* Software Requirements */

2011-05-07T11:50:15Z

Software Requirements

← Older revision		Revision as of 11:50, 7 May 2011
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	FusionSeq requires several additional packages to be installed in order to carry out the analysis and visualize the results. Moreover, since its modularity, different programs would need specific libraries. Moreover, some data sets are also required for the analysis (see [[#Data Requirements\|Data Requirements]]). Here we describe the complete set of tools that one would need to run the analysis as we do in our lab. The modules should be installed in the listed order.		FusionSeq requires several additional packages to be installed in order to carry out the analysis and visualize the results. Moreover, since its modularity, different programs would need specific libraries. Moreover, some data sets are also required for the analysis (see [[#Data Requirements\|Data Requirements]]). Here we describe the complete set of tools that one would need to run the analysis as we do in our lab. The modules should be installed in the listed order.

	'''Note''': the following instructions apply if one wants to compile FusionSeq from the source code (all versions). Alternatively, one can download the binaries (version 7.0 and later).		'''Note''': the following instructions apply if one wants to compile FusionSeq from the source code (all versions). Alternatively, one can download the [[FusionSeq_Download#Binaries\|binaries]] (version 7.0 and later).

	===Alignment tools===		===Alignment tools===

Asboner: /* (versions 0.7.0 and later -- coming soon) */

2011-05-07T11:46:52Z

(versions 0.7.0 and later -- coming soon)

← Older revision		Revision as of 11:46, 7 May 2011
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	===Scientific and bioinformatics libraries===		===Scientific and bioinformatics libraries===
	* [http://www.gnu.org/software/gsl/ GNU Scientific Library (GSL)]: this library is a required for the compilation of [http://rnaseq.gersteinlab.org/doc/bios/ BIOS].		* [http://www.gnu.org/software/gsl/ GNU Scientific Library (GSL)]: this library is a required for the compilation of [http://rnaseq.gersteinlab.org/doc/bios/ BIOS].
	=====(versions 0.7.0 and later ~~-- coming soon~~)=====		=====(versions 0.7.0 and later)=====
	* Starting with version 0.7.0, two new libraries are required:		* Starting with version 0.7.0, two new libraries are required:
	** [http://rnaseq.gersteinlab.org/doc/bios/ libbios], which replaces the old BIOS, can be downloaded [http://rnaseq.gersteinlab.org/fusionseq/tarballs/libbios-1.1.0.tar.gz here].		** [http://rnaseq.gersteinlab.org/doc/bios/ libbios], which replaces the old BIOS, can be downloaded [http://rnaseq.gersteinlab.org/fusionseq/tarballs/libbios-1.1.0.tar.gz here].
	** [http://rnaseq.gersteinlab.org/doc/mrf/ libmrf] can be downloaded [http://rnaseq.gersteinlab.org/fusionseq/tarballs/libmrf-1.0.0.tar.gz here]		** [http://rnaseq.gersteinlab.org/doc/mrf/ libmrf] can be downloaded [http://rnaseq.gersteinlab.org/fusionseq/tarballs/libmrf-1.0.0.tar.gz here]
			Please note that this libraries are for the "early access" version of FusionSeq.

	=====(versions up to 0.6.1)=====		=====(versions up to 0.6.1)=====
	* [http://rnaseq.gersteinlab.org/doc/bios/ BIOS] library: this library can be downloaded as part of [http://rseqtools.gersteinlab.org RSEQtools], a computational framework to analyze RNA-Seq data, or it can be downloaded as a separate component from [http://rnaseq.gersteinlab.org/fusionseq/tarballs/bios_0.9.0.tar.gz here].		* [http://rnaseq.gersteinlab.org/doc/bios/ BIOS] library: this library can be downloaded as part of [http://rseqtools.gersteinlab.org RSEQtools], a computational framework to analyze RNA-Seq data, or it can be downloaded as a separate component from [http://rnaseq.gersteinlab.org/fusionseq/tarballs/bios_0.9.0.tar.gz here].

Asboner: /* (versions up to 0.6.1) */

2011-05-07T11:45:21Z

(versions up to 0.6.1)

← Older revision		Revision as of 11:45, 7 May 2011
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	Instructions to install [http://www.gnu.org/software/gsl/ GSL] and [http://rnaseq.gersteinlab.org/doc/bios/ BIOS] can be found in '''[[Installation and Configuration of FusionSeq]]'''. However, please ensure that you read all the requirements (including [[#Data_requirements\|Data requirements]]) and downloaded all the libraries and packages needed.		Instructions to install [http://www.gnu.org/software/gsl/ GSL] and [http://rnaseq.gersteinlab.org/doc/bios/ BIOS] (or libbios and libmrf -- depending on the version) can be found in '''[[Installation and Configuration of FusionSeq]]'''. However, please ensure that you read all the requirements (including [[#Data_requirements\|Data requirements]]) and downloaded all the libraries and packages needed.

	===Drawing tools===		===Drawing tools===

Asboner: /* Scientific and bioinformatics libraries */

2011-05-06T22:14:50Z

Scientific and bioinformatics libraries

← Older revision		Revision as of 22:14, 6 May 2011
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	===Scientific and bioinformatics libraries===		===Scientific and bioinformatics libraries===
	* [http://www.gnu.org/software/gsl/ GNU Scientific Library (GSL)]: this library is a required for the compilation of ~~the~~ [http://rnaseq.gersteinlab.org/doc/bios/ BIOS].		* [http://www.gnu.org/software/gsl/ GNU Scientific Library (GSL)]: this library is a required for the compilation of [http://rnaseq.gersteinlab.org/doc/bios/ BIOS].
	* [http://rnaseq.gersteinlab.org/doc/bios/ BIOS]: this library can be downloaded as part of [http://rseqtools.gersteinlab.org RSEQtools], a computational framework to analyze RNA-Seq data, or it can be downloaded as a separate component from [http://rnaseq.gersteinlab.org/fusionseq/tarballs/bios_0.9.0.tar.gz here].		=====(versions 0.7.0 and later -- coming soon)=====
			* Starting with version 0.7.0, two new libraries are required:
			** [http://rnaseq.gersteinlab.org/doc/bios/ libbios], which replaces the old BIOS, can be downloaded [http://rnaseq.gersteinlab.org/fusionseq/tarballs/libbios-1.1.0.tar.gz here].
			** [http://rnaseq.gersteinlab.org/doc/mrf/ libmrf] can be downloaded [http://rnaseq.gersteinlab.org/fusionseq/tarballs/libmrf-1.0.0.tar.gz here]
			=====(versions up to 0.6.1)=====
			* [http://rnaseq.gersteinlab.org/doc/bios/ BIOS] library: this library can be downloaded as part of [http://rseqtools.gersteinlab.org RSEQtools], a computational framework to analyze RNA-Seq data, or it can be downloaded as a separate component from [http://rnaseq.gersteinlab.org/fusionseq/tarballs/bios_0.9.0.tar.gz here].


	Instructions to install [http://www.gnu.org/software/gsl/ GSL] and [http://rnaseq.gersteinlab.org/doc/bios/ BIOS] can be found in '''[[Installation and Configuration of FusionSeq]]'''. However, please ensure that you read all the requirements (including [[#Data_requirements\|Data requirements]]) and downloaded all the libraries and packages needed.		Instructions to install [http://www.gnu.org/software/gsl/ GSL] and [http://rnaseq.gersteinlab.org/doc/bios/ BIOS] can be found in '''[[Installation and Configuration of FusionSeq]]'''. However, please ensure that you read all the requirements (including [[#Data_requirements\|Data requirements]]) and downloaded all the libraries and packages needed.

Asboner: /* Software Requirements */

2011-05-06T22:01:36Z

Software Requirements

← Older revision		Revision as of 22:01, 6 May 2011
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	{{FusionSeqHeader}}		{{FusionSeqHeader}}
	==Software Requirements==		==Software Requirements==
	FusionSeq requires several additional packages to be installed in order to carry out the analysis and visualize the results. Moreover, since its modularity, different programs would need specific libraries. Moreover, some data sets are also required for the analysis (see [[#Data Requirements\|Data Requirements]]). Here we describe the complete set of tools that one would need to run the analysis as we do in our lab. The modules should be installed in the listed order.		FusionSeq requires several additional packages to be installed in order to carry out the analysis and visualize the results. Moreover, since its modularity, different programs would need specific libraries. Moreover, some data sets are also required for the analysis (see [[#Data Requirements\|Data Requirements]]). Here we describe the complete set of tools that one would need to run the analysis as we do in our lab. The modules should be installed in the listed order.

			'''Note''': the following instructions apply if one wants to compile FusionSeq from the source code (all versions). Alternatively, one can download the binaries (version 7.0 and later).

	===Alignment tools===		===Alignment tools===