Hi
I'm going to ask about bowtie2's mapping quality calculation for ChIP-Seq data. For sequences which align multiple locations Bowtie2 gives the MAPQ 30. It says for multiple aligned sequences, mapq is not meaningful, so why it gives 30 for all? Other thing it gives 30 for completely aligned sequence and sequences which has indels too. What is that 30 and why?
I attached a png file about my ask.
I'm going to ask about bowtie2's mapping quality calculation for ChIP-Seq data. For sequences which align multiple locations Bowtie2 gives the MAPQ 30. It says for multiple aligned sequences, mapq is not meaningful, so why it gives 30 for all? Other thing it gives 30 for completely aligned sequence and sequences which has indels too. What is that 30 and why?
I attached a png file about my ask.
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