Hi all, ive encountered a problem while working on miRNA expression analysis from an illumina run. usually when i work on the illumina sequence data, i remove all the reads that do not map to anywhere in the reference sequence or that have multiple alignments (non unique). this leaves me with only the uniquely mapped reads to analyze, which reduces the ambiguity of the results and makes the analysis more conclusive.
BUT, it seems that when aligning to miRNA reference (miRBase) there are miRNAs in the reference that are very similar, so similar that most of the reads that align to one of them, aligns to the others as well thus causing the reads to be non unique and to be discarded.
this of course cause a major deviation in the expression results and must be delt with.
how do you suggest i should deal with this issue?