{"id":588,"date":"2013-05-02T09:36:19","date_gmt":"2013-05-02T09:36:19","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=588"},"modified":"2017-06-14T13:28:04","modified_gmt":"2017-06-14T13:28:04","slug":"tophat","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/tophat\/","title":{"rendered":"TopHat"},"content":{"rendered":"

Overview<\/h2>\n

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.<\/p>\n

Versions 2.0.7, 2.0.9 and 2.0.14 binaries are available.<\/p>\n

Restrictions on use<\/h2>\n

All users may access and use Bowtie. The software is open source. Users should consult the following file for further information: $TOPHAT_HOME\/$TOPHAT_VER\/COPYING<\/p>\n

Set up procedure<\/h2>\n

To use the software you must load one<\/em> of the modulefiles:<\/p>\n

\r\nmodule load apps\/binapps\/tophat\/2.0.14\r\nmodule load apps\/binapps\/tophat\/2.0.9\r\nmodule load apps\/binapps\/tophat\/2.0.7\r\n<\/pre>\n
Running the application<\/h2>\n
Please do not run tophat on the login node. Jobs should be submitted to the compute nodes via batch. If you wish to see the available command-line flags that tophat accepts you can run the following on the login node:<\/p>\n
\r\ntophat --help\r\n<\/pre>\n
Serial batch job submission<\/h3>\n
Ensure you have loaded one of the above modulefiles. Then create a jobscript similar to:<\/p>\n
\r\n#!\/bin\/bash\r\n#$ -V\r\n#$ -cwd\r\n\r\n# $NSLOTS will be set to 1 in a serial job\r\ntophat --num-threads $NSLOTS -O OUTPUT_DIRECTORY<\/em> -G DIRECTORY_FOR_GTF\/GFF_FILE<\/em> \\\r\n       --library-type fr-firststrand INDEXES_DIRECTORY<\/em>\r\n<\/pre>\n
Submit the jobscript to the batch system using<\/p>\n
\r\nqsub jobscript<\/em>\r\n<\/pre>\n
where jobscript<\/em><\/code> is the name of your batch submission file.<\/p>\n
Parallel batch job submission<\/h3>\n
Ensure you have loaded one of the above modulefiles. Then create a jobscript similar to:<\/p>\n
\r\n#!\/bin\/bash\r\n#$ -V\r\n#$ -cwd\r\n#$ -pe smp.pe 8     # Between 2-24 cores permitted\r\n\r\n# $NSLOTS will be set automatically to the number given above on the pe line\r\ntophat --num-threads $NSLOTS -O OUTPUT_DIRECTORY<\/em> -G DIRECTORY_FOR_GTF\/GFF_FILE<\/em> \\\r\n       --library-type fr-firststrand INDEXES_DIRECTORY<\/em>\r\n<\/pre>\n
Submit the jobscript to the batch system using<\/p>\n
\r\nqsub jobscript<\/em>\r\n<\/pre>\n
where jobscript<\/em><\/code> is the name of your batch submission file.<\/p>\n
Linking with other applications<\/h3>\n
It may be necessary to use other applications in conjunction with Tophat. <\/p>\n
Panagiotis Papastamoulis, from FLS has very kindly provided some documentaion illustrating how to use Cufflinks on the CSF<\/a>. This may be a useful reference as it does include some Tophat examples and jobscripts.<\/p>\n
Further info<\/h2>\n