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Old 10-25-2012, 11:13 PM   #1
hanshart
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Location: Germany

Join Date: Nov 2011
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Default Bowtie2 / Bowtie 2 multiseed strategy

Hi everyone,
I have a question about Bowtie2's multiseeding. How is Bowtie2 handling seeds that overlap the end of the read (because they are longer than the read or because of the intervall-shifting of the seeds)? Are those seeds ignored or are they used truncated?

2 Examples:
1) What happens if the read length is 20 bp and you choose a seed greater than this, e.g. 22 bp. Are just the first 20 bases taken as seed?
2) read length: 20 bp, seed length: 15 bp, intervall length: 10 bp. Is only the first seed used or is also the second one used with only 10 bases?

Thank you

Last edited by hanshart; 10-25-2012 at 11:15 PM.
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