How to add number to output file by iteration?

Question

linux

Hello, I have three files in the B4627 directory:

1_S_R1_001.fastq.gz
2_S_R1_001.fastq.gz
3_S_R1_001.fastq.gz

I need my script to perform an operation with each of the files and the output is the corresponding fileexit_1.sam, exit_2.sam, exit_3.sam

#!/bin/bash

for FILE in *R1_001.fastq.gz;

do
BASENAME=${file%%_R1_001.fastq.gz*}
        echo   "bowtie2 -x covexp -U B4627/$FILE -S exit.sam" ;
done

To separate numbers in files, I can only think of this for now: what do I need to add to the script so that only its number is displayed with each file? Thanks PS Of course, the echo in the script is just to check if the loop is working properly..

ls -l | awk '{print $9}' | sed 's/_S.*$//'

exit.sam

Answer 1

for i in *R1_001.fastq.gz;do basename $i _S_R1_001.fastq.gz;done