I am quite new to NGS data analysis, I want to map small RNA seq to reference genome. I used SRA small RNA seq samples, particularly miRNA seq to miRbase genome index and piRNA to piRbase genome index. but I could not find a mapping results more than 5% for any samples even for already published SRA samples. I want to ask what method should I use or what mistake I could be doing.
I used normal bowtie mapping command
bowtie2 -x miRbase or piRBase index -U SRR3303398.fastaq -S output.sam