discrepancy in two known miRNA results in miRDeep2

Question

[SJ Basu]

Hello people,

I ran miRDeep2 program on a plant small rna data. After inspecting the outputs I found there are two output file with regard to known miRNA found in the data first is result_29_01_2017_t_18_17_09.csv second is miRNAs_expressed_all_samples_29_01_2017_t_18_17_09.csv ...After going through the files, I found that the reported miRNAs differed in both nature and number, i.e., result file had 30 miRNAs while expressed file had 52 miRNAs ...I check through bowtie output that both are correctly reporting but to what reasons do we attribute this difference ? which one should be considered if both target prediction and simple mirna profile discovery are my concern ?

Any suggestion is much appreciated.