FusionSeq Requirements
From GersteinInfo
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* [http://bowtie-bio.sourceforge.net/index.shtml bowtie] (64bit) | * [http://bowtie-bio.sourceforge.net/index.shtml bowtie] (64bit) | ||
* [http://users.soe.ucsc.edu/~kent/src/ Blat (source)] [http://genome-test.cse.ucsc.edu/~kent/exe/ (binaries)] | * [http://users.soe.ucsc.edu/~kent/src/ Blat (source)] [http://genome-test.cse.ucsc.edu/~kent/exe/ (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 | + | 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=== | ===Scientific and bioinformatics libraries=== | ||
Revision as of 14:40, 19 August 2010
User documentation main
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.
Contents |
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.
