tophat-software
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tophat-software [2014/10/17 08:28] – joguya | tophat-software [2015/07/23 09:38] (current) – joguya | ||
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====== TopHat ====== | ====== TopHat ====== | ||
- | * TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. | + | TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. |
- | * Link: http:// | + | |
- | + | | |
- | ===== v2.0.13 ===== | + | * Added: |
- | | + | |
- | * Added: | + | |
* Link: http:// | * Link: http:// | ||
- | * Version 2.0.13 is a maintenance release with the following changes: | ||
- | - removed SAMtools as an external dependency in order to avoid incompatibility issues with recent and future changes of SAMtools and its code library (an older, stable SAMtools version is now packaged with TopHat) | ||
- | - fixed a few code compatibility issues when compiling on OSX 10.9 | ||
- | ==== Usage ==== | + | === Usage === |
- | * show available versions: < | + | * Show all available versions |
+ | * Load tophat module: < | ||
- | ---------------------------------------------------------------------------------------------- | + | === Installation === |
- | tophat2/2.0.11 tophat2/2.0.13 tophat2/ | + | *Tophat2 is already compiled, just download the tarball & copy content to /export/apps< |
+ | wget http:// | ||
+ | tar -xvf tophat-2.1.0.Linux_x86_64.tar.gz | ||
+ | cd tophat-2.1.0.Linux_x86_64/ | ||
+ | sudo mkdir / | ||
+ | sudo cp -r . / | ||
</ | </ | ||
- | * load v2.0.13:< | ||
- | * show help info:< | ||
- | |||
- | ==== Installation ==== | ||
- | > **NOTE** | ||
- | > Older versions of tophat2 required SAMtools to be loaded/ | ||
- | |||
- | * < | ||
- | tar -xvf tophat-2.0.13.Linux_x86_64.tar.gz | ||
- | sudo mkdir / | ||
- | cp -rv tophat-2.0.13.Linux_x86_64/ | ||
- | * create module file:< | ||
- | ##################################################################### | ||
- | ## | ||
- | ## tophat Modulefile | ||
- | ## by James Oguya, < | ||
- | ## October, 2014 | ||
- | ## | ||
- | |||
- | set appname | ||
- | set version | ||
- | set prefix | ||
- | set exec_prefix | ||
- | set url " | ||
- | set msg " | ||
- | |||
- | proc ModulesHelp { } { | ||
- | puts stderr " | ||
- | } | ||
- | |||
- | module-whatis | ||
- | |||
- | conflict tophat tophat2 | ||
- | |||
- | prepend-path | ||
- | |||
- | # tophat v2.0.13 removed SAMtools as an external dependency in order to avoid incompatibility issues with recent and future changes of SAMtools and its code library (an older, stable SAMtools version is now packaged with TopHat)</ | ||
- | |||
- | * deploy using ansible< | ||
- | |||
- |
tophat-software.1413534502.txt.gz · Last modified: 2014/10/17 08:28 by joguya