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Old 03-05-2012, 12:21 PM   #1
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Location: Philadelphia

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Default What is a good mapping quality cutoff?

I am analyzing a ChIP-Seq dataset and was considering filtering reads based on mapping quality. I am not sure what threshold is the most appropriate in practical cases.

Also, I am really confused by the range, I have done two sets of alignments, one with Bowtie and other with Bowtie2. In the first set all the mapping qualities are 255, while with Bowtie 2 the qualities range from 1-42 (for the same set of reads. Why is it?

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Old 03-06-2012, 07:28 AM   #2
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I don't think Bowtie computes mapping qualities. A MQ should be between 1-60 based on my experience.

BWA, Stampy, Clc etc give me (via Samtools) more realistic mapping qualities.

It seems bowtie2 does give you MQ though, interesting.
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