bash loop to count multiple words from multiple corresponding files

[chayan]

I have generated multiple read mapping files (.sam) generated with bowtie2 "--no-unal" parameter. As the number of files are huge (7 reference genomes mapped against >6000 reads) i want a loop to count the % (or total number) mapped reads for each file.

HTSeq could be an option but don't know how to loop it for multiple files.
Any help would be much appreciated.

[GenoMax]

You should consider using featureCounts. You may not need a loop. You can feed all SAM files to featureCounts and generate a read count matrix directly.

featureCounts <options> file1.sam file2.sam file3.sam etc.