Hi,

I have paired end data which im trying to align using tophat:

tophat -r 200 -p 4 -o /.../Tophat_output/ -G /pathtogtf  /pathtobowtieindexfiles Sample10_untrim1.fastq Sample10_untrim2.fastq

Im getting only one bam alignment file. Im not sure if I should be getting 2 bam files. 
You should get the accepted bam file, and another one of unmapped sequences

But don't expect two bam accepted files, one for each of the paired sequences. You only get one
