What is a good mapping quality cutoff?

[LP_SEP23]

Hi
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?

thanks

[colindaven]

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.