Then check the following command out: scc4% tophat -o tophat_st_out $SCC_TOHHAT_EXAMPLES/test_data/test_ref $SCC_TOHHAT_EXAMPLES/test_data/reads_1.fq $SCC_TOHHAT_EXAMPLES/test_data/reads_2.fq
The above command will use the test data provided in Tophat examples directory to show the simple tophat command to align two paired read files (reads_1.fq, and reads_2.fq). The alignment result is put at 'tophat_st_out/' under current directory.
To submit a job, execute command: scc4% qsub -P my_project my_tophat_job.qsub
When running TopHat with paired reads it is critical that the *_1 files an the *_2 files appear in separate comma-delimited lists, and that the order of the files in the two lists is the same. Usage: tophat [options]* <genome_index_base> <reads1_1[,...,readsN_1]> [reads1_2,...readsN_2]
As of the date, TopHat can align reads that are up to 1024 bp long.
It's NOT recommended to mix pair-end and single end reads together in one run, for it will give sub-optimal result.
TopHat's default values for paramteres are tuned for processing mammalian RNA-Seq reads. For other species/organism, it's recommended to set some of the parameters with more strict, conservative values than their defaults.