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I am doing single end alignment with bowtie. I don't want any mismatches and I only want to keep reads that mapped uniquely. I used the options -v 0 and -m 1. The issue I am having is that it seems that bowtie is not actually suppressing reads with more than 1 reportable alignments. Here is a part of the output log.
# reads processed: 685653
# reads with at least one reported alignment: 420799 (61.37%)
# reads that failed to align: 134703 (19.65%)
# reads with alignments suppressed due to -m: 130151 (18.98%)
Reported 420799 alignments to 1 output stream(s)
What I am trying to understand is why alignments that are supposed to be suppressed by -m are still being reported. In the above example, I want only 290648 reads to be outputted. Is it necessary to do further filtering to remove these reads?
Thank you,
Annie
# reads processed: 685653
# reads with at least one reported alignment: 420799 (61.37%)
# reads that failed to align: 134703 (19.65%)
# reads with alignments suppressed due to -m: 130151 (18.98%)
Reported 420799 alignments to 1 output stream(s)
What I am trying to understand is why alignments that are supposed to be suppressed by -m are still being reported. In the above example, I want only 290648 reads to be outputted. Is it necessary to do further filtering to remove these reads?
Thank you,
Annie
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