If reads can be mapped to several equally best positions, tools like MAQ will randomly choose one position and give the alignment a zero mapping quality and you cannot see all the hits of the read against the reference sequence.
In my case I want to know all the positions of the reads that mapped to those equally best positions.
Does anyone know a tool that can solve this problem?
In my case I want to know all the positions of the reads that mapped to those equally best positions.
Does anyone know a tool that can solve this problem?
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