From GersteinInfo

Revision as of 12:56, 19 August 2010 (view source) Asboner (Talk | contribs) (→Software Requirements) ← Older edit		Revision as of 13:04, 19 August 2010 (view source) Asboner (Talk | contribs) (→Data Requirements) Newer edit →
Line 6:		Line 6:
	==[[Software Requirements]]==		==[[Software Requirements]]==
-	==Data Requirements==	+	==[[Data Requirements]]==
-		+
-	Here is the list of required data for a comprehensive use of FusionSeq tools.	+
-		+
-	===External===	+
-	*[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:	+
-	$ bowtie-build -f hg18_nh.fa /path2bowtieIndex/hg18_nh/	+
-	where hg18_nh.fa corresponds to the concatenation of all human chromosomes from chromFa.zip without the different haplotypes and "random" stuff.	+
-		+
-	===Provided===	+
-	The following data sets, bundled in a tarball, can be downloaded [http://rnaseq.gersteinlab.org/tarballs/FusionSeq_Annotation_Data_1.0.tar.gz here].	+
-	* knownGeneAnnotation.txt	+
-	* knownGeneAnnotationTranscriptCompositeModel.txt	+
-	* knownGeneAnnotationTranscriptCompositeModel.fa	+
-	* kgXref.txt	+
-	* knownToTreefam.txt	+
-		+
-	The composite model needs to be indexed by bowtie:	+
-	$ bowtie-build -f knownGeneAnnotationTranscriptCompositeModel.fa /path2bowtieIndex/hg18_knownGeneAnnotationTranscriptCompositeModel/hg18_knownGeneAnnotationTranscriptCompositeModel	+
-		+
-	Please make sure that the correct filenames are used.	+
	=[[Download]]=		=[[Download]]=

---

Revision as of 13:04, 19 August 2010

FusionSeq main web page

Contents 1 Introduction 1.1 Software Requirements 1.2 Data Requirements 2 Download 3 Installation and Configuration of FusionSeq 4 How to execute FusionSeq

Introduction

This page provides the source code for FusionSeq. Please note that these tools were tested on a multi-node cluster of computing nodes with Linux Red Hat as operating system and PBS as scheduler system. FusionSeq programs are written in C and should likely compile to most Unix/Linux platforms. We used the gcc complier (version 3.4.6 20060404) to compile the source code. However, this is not a plug-and-play program, but it requires the user to compile, install and run a set of programs. Please read the requirements before downloading FusionSeq.

Software Requirements

Data Requirements

Download

Installation and Configuration of FusionSeq

How to execute FusionSeq

---

last revision: 12:53, 19 August 2010 (UTC)