I am relatively new to the sequencing analysis with some experience with RNA-seq. I have six samples from a non model plant species which were sequenced for small RNA analysis. miRNA to be specific. After going through different articles, I was able to filter the reads using different criteria like quality, size, discarding reads aligning on other RNA types etc. And then aligned the filtered reads to plant miRNA sequences from mirbase (mature.fa).
I got stuck when I tried to quantify the identified miRNA for expression. There are multiple cases where a particular miRNA sequence have multiple different miR ID. So I seek help on how to assign the unique miR id to these cases. (Not the miR family id).
I searched online and read multiple articles but no luck. Seek help. Thanks in advance.