I recently switched from using bwa to using bowtie for aligning reads to hg19. Using bwa I filtered out MAPQ score below 30. This seems like a fairly common practice. Bowtie does not have a similar score. Is it common practice to accept all bowtie alignments?
Note - For both bwa and bowtie, I filter out unmapped reads as well as reads that map to multiple locations.
Note - For both bwa and bowtie, I filter out unmapped reads as well as reads that map to multiple locations.