How to build the fly genome in Bowtie

[lilithdog]

Sorry this is such a basic question, but several people have given me different answers and none so far have worked. I am trying to align the various chromosome parts for further sequence alignment work. I have tried various commands, listing of the files themselves, listing the path of the files and *.fa (as all the files are in fastA format). When I list the path, the program tells me it can't read it.

I just need some good help, please...

[lilithdog]

Thanks, but I sort of figured it out.