In summary: I will show which is the best miRNA mapping tool. I used several options for this benchmarking:
I think that these are the most used, and other not used but good to try them. They were clearly developed for other purposes, but as well, they generate the input of many miRNA pipelines. I just wanted to know how well my tool was doing. The first aim to develop miraligner was to get annotated additions of nucleotides at the end of miRNA sequences, something that is very common in mirna biogenesis: isomirs and often they are missed by short read and fast mappers. I have a repository for this kind of things, so anybody can reproduce my results, and check if I did something wrong, or comment on it. In this post I just want to know which tool detects more miRNA, for that I did two main steps: