The well known sloice-aware aligner or mapper, now being phased out in favour of HISAT2
module load tophat
This will load the latest version (2.1.1 from 2016). To see the help:
Note the reference to the webpage at the end, that proves to be an easier help resource. As it's some what long, the important parts are extracted here.
The tophat script produces a number of files in the directory in which it was invoked. Most of these files are internal, intermediate files that are generated for use within the pipeline. The output files you will likely want to look at are:
accepted_hits.bam, A list of read alignments in binary SAM format. This is the chief output file.
junctions.bed, A UCSC BED track of junctions reported by TopHat. Each junction consists of two connected BED blocks, where each block is as long as the maximal overhang of any read spanning the junction. The score is the number of alignments spanning the junction.
deletions.bed. UCSC BED tracks of insertions and deletions reported by TopHat.
insertions.bed- chromLeft refers to the last genomic base before the insertion.
deletions.bed- chromLeft refers to the first genomic base of the deletion.