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Old 05-07-2012, 05:39 AM   #4
Senior Member
Location: Berlin

Join Date: Jul 2011
Posts: 156

Well, using the settings (default or your specific choices), Bowtie found no reportable alignment for that read.
It is not possible to make a general statement about this behaviour here as it depends entirely on the settings you provided bowtie with and the nature of your reads and reference. Check the bowtie manual, typically you should look at alignment and reporting modes - these and their sub-options control alignment sensitivity and reporting filters.
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