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TopHat
Overview
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.
Versions 2.0.7, 2.0.9 and 2.0.14 binaries are available.
Restrictions on use
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
Set up procedure
To use the software you must load one of the modulefiles:
module load apps/binapps/tophat/2.0.14 module load apps/binapps/tophat/2.0.9 module load apps/binapps/tophat/2.0.7
Running the application
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:
tophat --help
Serial batch job submission
Ensure you have loaded one of the above modulefiles. Then create a jobscript similar to:
#!/bin/bash #$ -V #$ -cwd # $NSLOTS will be set to 1 in a serial job tophat --num-threads $NSLOTS -O OUTPUT_DIRECTORY -G DIRECTORY_FOR_GTF/GFF_FILE \ --library-type fr-firststrand INDEXES_DIRECTORY
Submit the jobscript to the batch system using
qsub jobscript
where jobscript is the name of your batch submission file.
Parallel batch job submission
Ensure you have loaded one of the above modulefiles. Then create a jobscript similar to:
#!/bin/bash #$ -V #$ -cwd #$ -pe smp.pe 8 # Between 2-24 cores permitted # $NSLOTS will be set automatically to the number given above on the pe line tophat --num-threads $NSLOTS -O OUTPUT_DIRECTORY -G DIRECTORY_FOR_GTF/GFF_FILE \ --library-type fr-firststrand INDEXES_DIRECTORY
Submit the jobscript to the batch system using
qsub jobscript
where jobscript is the name of your batch submission file.
Linking with other applications
It may be necessary to use other applications in conjunction with Tophat.
Panagiotis Papastamoulis, from FLS has very kindly provided some documentaion illustrating how to use Cufflinks on the CSF. This may be a useful reference as it does include some Tophat examples and jobscripts.
Further info
- The Tophat website has a manual, FAQ and index and annotations downloads.
- Related applications available on the CSF: