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Hi,
I have a question about how bowtie2 works in aligning pairs. For example, I have a pair of mates. Mate 1 only has one unique alignment, but mate 2 can be mapped to multiple locations with the same alignment scores. And I set parameters as --no-mixed --no-discordant --X 500. Here are my questions:
1, From the manual, it says that the default model is to search for multiple alignments and report the best one. Since mate2 has multiple equally good alignments, will bowtie2 just report one of those alignments randomly?
2, Among those multiple equally good alignments of mate2, let's say some alignment can satisfy the distance constraints defined by -X 500, but some can't. If bowtie2 report one of those alignment randomly, can I understand it this way? If the reported alignment of mate2 happened to satisfy the distance constraints, then the pair will be considered as a valid pair. But if the reported alignment of mate2 happened to beyond the distance constraints, then the pair will be discarded?
Thank you!
The text was updated successfully, but these errors were encountered:
Hi,
I have a question about how bowtie2 works in aligning pairs. For example, I have a pair of mates. Mate 1 only has one unique alignment, but mate 2 can be mapped to multiple locations with the same alignment scores. And I set parameters as --no-mixed --no-discordant --X 500. Here are my questions:
1, From the manual, it says that the default model is to search for multiple alignments and report the best one. Since mate2 has multiple equally good alignments, will bowtie2 just report one of those alignments randomly?
2, Among those multiple equally good alignments of mate2, let's say some alignment can satisfy the distance constraints defined by -X 500, but some can't. If bowtie2 report one of those alignment randomly, can I understand it this way? If the reported alignment of mate2 happened to satisfy the distance constraints, then the pair will be considered as a valid pair. But if the reported alignment of mate2 happened to beyond the distance constraints, then the pair will be discarded?
Thank you!
The text was updated successfully, but these errors were encountered: