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BenLangmead / bowtie

An ultrafast memory-efficient short read aligner
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wrong number of reads processed #70

Closed sklasfeld closed 6 years ago

sklasfeld commented 6 years ago

When I input paired end reads each with 44 million reads, bowtie reports that it processed 67 million reads. The only parameters I used were --no-unal -S --chunkmbs 200 --best -m 1. I had installed bowtie from bowtie-1.2.1.1-linux-x86_64.zip. Any ideas of why this is the case?

ch4rr0 commented 6 years ago

This is a known bug in this version of bowtie. We have already pushed a commit for the issue that will be in the next bowtie release. In the meantime you can try using the beta build available here.

ndaniel commented 6 years ago

This is probably the same as this: https://github.com/BenLangmead/bowtie/issues/55

ch4rr0 commented 6 years ago

This change was included as part of our most recent release.