Bash: replace part of filename

Question

I have a command I want to run on all of the files of a folder, and the command\'s syntax looks like this:

tophat -o  
         


        

Answer 1

Alternative to anubhava's concise solution,

d=$(dirname path/to/sample1.fastq)
b=$(basename path/to/sample1.fastq .fastq)
echo $d/$b.fastq
path/to/sample1.fastq

tophat -o "$d/$b.fastq" "$f"