#3 miRNA expression analysis

[Ruchi]

Hi,
I am currently analysing UMI-smallRNAseq data for novel miRNA prediction. I predicted 106 novel miRNA from this dataset and plot PCA which does not give biological fesible result. I am describing here how I did my analysis with this tool miRDP2.
1> clean reads and collapsed by fastx
2> miRDP2 run by giving reference genome and clean reads
3> select mature miRNA sequence (present in at least two replicate per sample) from prediction file (produced by miRDP2)
4> take novel miRNA mature sequence and made database of it
5> mapped clean reads over it and generate count file
6> this count file used for PCA plot.

I following questions regarding this:

Is this way to get expression value or any other way to do that?
Is it possible to get miRNA with same similar sequence (one is upper case (coding region) and another one is lower case (repeatitive region)) and mapped in different genomic location. I am getting this type of miRNA as well.

Could you please help me in this?

Thanks