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

You can use:

tophat -o "${f/.fastq/.bam}" "$f"

Testing:

f='path/to/sample1.fastq'
echo "${f/.fastq/.bam}"
path/to/sample1.bam