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Old 12-08-2011, 01:03 AM   #1
gavin.oliver
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Default Bfast, single end reads and large indels

Hi,

I am wondering what the largest indels I can theoretically detect with Bfast and single end 90bp reads are? Has anyone got experience in this? Come on Nils - I know you must have
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Old 12-08-2011, 08:59 AM   #2
HESmith
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If you're willing to try an alternative approach, we've mapped 15 and 97 kb deletions using split-end alignment (essentially, treating the 5' and 3' ends of your reads as paired-end). It's described here.
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