Permission denied error using sed to change file name

I'm trying to take the filename of each file in a directory and 'rename' it to create a respective output file when running through a program. When running the script I get the error Permission denied, for the line that is meant to be doing the renaming.

outputname=basename $file | sed -e "s/_Aligned.sortedByCoord.out.bam/_.gtf/"

For example one file is named 92_Aligned.sortedByCoord.out.bam, I want the output to be 92_.gtf. Another file is called 10.5_rep1_Aligned.sortedByCoord.out.bam, and the output should be called 10.5_rep1_.gtf.

Am I doing it wrong? Not sure if sed is the right way as I'm technically not renaming the file, but creating another file from that name and changing it?

You want to force evaluation on basename-sed pipe. ( with '$(' ) and handle the quoting)

outputname=$(basename $file | sed -e "s/_Aligned.sortedByCoord.out.bam/_.gtf/")

Or using Bash built-in only, which will be much FASTER.

file_base=${file##*/}
outputname=${file_base/_Aligned.sortedByCoord.out.bam/_.gtf}