I have two questions concerning the HISAT2 tool installed in Galaxy:
How can I increase sensitivity in order to allow for alignment mismatches between viral reference genomes and target sequences in a data set? Since viral genomes exist in various strains and contain natural variations, we would like to be able to allow for a 10% mismatch between the reference genome and the target sequences within our data set. Please advice us as to how we can accomplish this.
Can HISAT2 be used for miRNA analysis? What is the best tool in Galaxy for this task?