If the following command line is used to generate the SAM file.
bowtie -q -v 0 -k 10 -S -t <index.name> <input.fastq> <out.sam>
featureCounts program will be used to count the reads by enabling the multi-mapping reads counting:
featureCounts -t miRNA -g Name -O -M -a <mirbasefile> -o <outfile> <samfiles>
I wonder how featureCounts with the tags such as -O and -M will hand this situation as we know that this SAM file doesn't have "NH" tag? Will the command line above work properly for the microRNA quantification?