tophat - basic question - mapped reads

[chrisbala]

Hi,

I've posted this question before but still don't have the answer. At least one other forum reader seconded my question... maybe we've just missed something obvious...

1) Where in the tophat output files can I find the # of mapped reads? IN bowtie this is easy to find, but I can't find this anywhere in the tophat output?

on a related note

2) Is it possible (and/or desirable) to adjust the bowtie mapping parameters when running tophat? Is this just done with the same options as in bowtie?

Thanks for your help!