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  • 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

  • #2
    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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