My goal is to a) find novel and known miRNA from the data and 2) perform DGE analysis
I therefore aligned my miRNA reads (after adapter trimming and removing reads less than 18 bp) to the genome of interest but the mapping percentage is extremely low- think 2%. I used miRDeep2's mapper.pl to align, which in turn uses bowtie. I looked into these parameters if I can relax any of them, but they seem reasonable. I proceeded with the next step, miRDeep2.pl, but the number of known miRNA reported is either 1 for some samples or 0.
This happened for all samples in the same run, as well as all samples from another from a different species.
I would like to know what can be the possible reasons for low mapping percentage and if I can use them for finding known/novel miRNA using miRDeep2. The individual quality of the bases is very good, so I don't think that mismatches are reason for this.
UPDATE: I anyway proceeded to use miRDeep2 to look for known/novel miRNA. The result.html file does not report any known miRNA to be present in the data, but the read counts are generated with the name of the known mature miRNA from miRBase I supplied. Now I'm thoroughly confused. Is it advisable to continue with these read counts for DGE?