in an effort to map RNA-seq reads directly onto the genome I set the gap opening and gap extension parameters of bwa both to 0 (-O0 and -E0) in order to allow for exon junctions. However, bwa still reports not only perfect matches but also distance 1 matches rather than gapped alignments. Can this behaviour be changes somehow? I want gapped and ungapped alignments (in case both are without mismatches) to be treated equal.
Any help would be greatly appreciated!