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
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
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