Bfast, single end reads and large indels

[gavin.oliver]

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

[HESmith]

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.