This is my first miRNA study. I'm focusing right now on differential expression of known miRNA genes. I am aligning the reads to the genome by running bowtie with the following parameters:
bowtie -n 0 -e 80 -l 18 -a -m 5 --best --strata
What I am concerned about is that only 10-30% of all reads map (percentage varies between the replicates). I checked few of the non-aligned reads and they seem to be mRNA. I presume the restrictive settings that I used prevented them from getting aligned to the genome.
I am doing just the bioinformatics analysis - shall I communicate to my wet lab colleague that this is a problem? Essentially my question is - shall we be worried about the low percentage of mappable miRNA in the samples? The quality of the data seems fine - judging the output of fastQC so it must be due to the way the biological material was captured and the library prepared. The study is on mice so I do not expect to stumble upon a lot of unknown miRNAs (which would have explained the low mappability). Let me know what you think.