BWA and short read mapping

[alessandromacc]

Dear developers,

I am currently working with miRNA-seq reads from Illumina platforms, which are very short reads, ranging from 16 to roughly 30 nucleotides, and I want to map them onto a reference database for miRNAs, much shorter than the reference genome.

Is there a specific reason, in your opinion, to claim that BWA can outperform other popular mappers like Bowtie, when it comes to this kind of short reads?

Are the default parameters suitable for miRNA sequencing analysis in your opinion?

Also, I am currently interested in counting all the alternative hits of each mapped read (those listed in the XA tag in the SAM records) for a differential expression analysis. After doing some research, I don't believe it to be possible to instruct BWA to write a separate SAM record for an alternative mapping of a read (say like Bowtie does by default).
Can you suggest how to count all the alignments reported by BWA in the SAM file (primary and alternative)?

Thank you kindly for your help!