Tophat options to report unaligned reads and controlling Bowtie options

[Siva]

I run Tophat from command line on our shared Linux environment queue. The gist is this:

$ ~/tophat -o ./tophat_out_s1 -p 4 --solexa1.3-quals ./genome_bwtind/<AGPv1_genome_ind> [B]s_1_sequence.txt[/B]

I supply the options -o (for output file) -p (no. of threads) and --solexa1.3-quals (specifying quality). I also specify the path to the bowtie index and finally the actual sequence.txt (fastq) file.

I understand that Tophat runs Bowtie twice. Can I supply an option to Tophat to only report the unaligned reads after its run? I mean something like the bowtie --un option. Similarly on these lines is it possible to control Bowtie paramters from the Tophat command?

thanks
Siva