FusionSeq Requirements
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| + | ==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. | ||
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===Data analysis=== | ===Data analysis=== | ||
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| + | ==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. | ||
Revision as of 14:43, 19 August 2010
User documentation main
Contents |
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). 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.
Alignment tools
- bowtie (64bit)
- Blat (source) (binaries)
Please make sure that blat and bowtie executables are part of the PATH, i.e. they can be accessed and executed from any location on your file system. Moreover, make sure that twoBitToFa is also downloaded from the blat package and part of the PATH.
Scientific and bioinformatics libraries
Drawing tools
Data analysis
Data Requirements
Here is the list of required data for a comprehensive use of FusionSeq tools.
External
- 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 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.
